Starting phenix.real_space_refine on Sat Jul 4 07:57:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3f_38880/07_2026/8y3f_38880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3f_38880/07_2026/8y3f_38880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y3f_38880/07_2026/8y3f_38880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3f_38880/07_2026/8y3f_38880.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y3f_38880/07_2026/8y3f_38880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3f_38880/07_2026/8y3f_38880.map" } resolution = 4.54 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= 0.004 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 500 5.49 5 S 26 5.16 5 C 11119 2.51 5 N 3778 2.21 5 O 4750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 20173 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 703 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 5160 Classifications: {'DNA': 250} Link IDs: {'rna3p': 249} Chain: "J" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 5090 Classifications: {'DNA': 250} Link IDs: {'rna3p': 249} Chain: "K" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "L" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 553 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "M" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "N" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "O" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" P DA I 134 " occ=0.50 ... (19 atoms not shown) pdb=" C4 DA I 134 " occ=0.50 residue: pdb=" P DC I 137 " occ=0.50 ... (17 atoms not shown) pdb=" C6 DC I 137 " occ=0.50 residue: pdb=" P DG I 142 " occ=0.50 ... (20 atoms not shown) pdb=" C4 DG I 142 " occ=0.50 residue: pdb=" P DC I 149 " occ=0.50 ... (17 atoms not shown) pdb=" C6 DC I 149 " occ=0.50 residue: pdb=" P DG J 102 " occ=0.50 ... (20 atoms not shown) pdb=" C4 DG J 102 " occ=0.50 residue: pdb=" P DC J 109 " occ=0.50 ... (17 atoms not shown) pdb=" C6 DC J 109 " occ=0.50 residue: pdb=" P DG J 114 " occ=0.50 ... (20 atoms not shown) pdb=" C4 DG J 114 " occ=0.50 residue: pdb=" P DT J 117 " occ=0.50 ... (18 atoms not shown) pdb=" C6 DT J 117 " occ=0.50 Time building chain proxies: 3.81, per 1000 atoms: 0.19 Number of scatterers: 20173 At special positions: 0 Unit cell: (108.78, 166.11, 148.47, 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 26 16.00 P 500 15.00 O 4750 8.00 N 3778 7.00 C 11119 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: 1.29 Conformation dependent library (CDL) restraints added in 327.6 milliseconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2330 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 17 sheets defined 75.9% alpha, 2.9% beta 233 base pairs and 398 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.624A 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 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.455A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.558A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 77 removed outlier: 3.511A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.696A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 17 through 22 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.425A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 89 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 37 through 49 Processing helix chain 'N' and resid 55 through 84 Processing helix chain 'N' and resid 90 through 102 Processing helix chain 'N' and resid 103 through 123 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 77 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'P' and resid 24 through 29 Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 Processing helix chain 'P' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.855A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.498A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 101 through 102 removed outlier: 6.736A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.868A 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: 7.639A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 Processing sheet with id=AB2, first strand: chain 'K' and resid 83 through 84 removed outlier: 7.304A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.241A pdb=" N ARG M 42 " --> pdb=" O ILE N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'M' and resid 101 through 102 removed outlier: 6.607A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'O' and resid 83 through 84 removed outlier: 7.719A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'O' and resid 118 through 119 712 hydrogen bonds defined for protein. 2088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 600 hydrogen bonds 1196 hydrogen bond angles 0 basepair planarities 233 basepair parallelities 398 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 1.70 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: 3127 1.33 - 1.45: 7572 1.45 - 1.57: 9810 1.57 - 1.69: 998 1.69 - 1.81: 44 Bond restraints: 21551 Sorted by residual: bond pdb=" C3' DC J 150 " pdb=" C2' DC J 150 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 bond pdb=" C3' DC J 139 " pdb=" C2' DC J 139 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DT J 241 " pdb=" C2' DT J 241 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DT I 105 " pdb=" C2' DT I 105 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DG I 179 " pdb=" C2' DG I 179 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 21546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 29774 2.05 - 4.10: 1386 4.10 - 6.15: 74 6.15 - 8.20: 17 8.20 - 10.25: 4 Bond angle restraints: 31255 Sorted by residual: angle pdb=" O4' DG I 92 " pdb=" C4' DG I 92 " pdb=" C3' DG I 92 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.70e+01 angle pdb=" O4' DA I 249 " pdb=" C4' DA I 249 " pdb=" C3' DA I 249 " ideal model delta sigma weight residual 106.00 102.95 3.05 6.00e-01 2.78e+00 2.58e+01 angle pdb=" O4' DA I 183 " pdb=" C4' DA I 183 " pdb=" C3' DA I 183 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.51e+01 angle pdb=" O4' DC J 81 " pdb=" C1' DC J 81 " pdb=" N1 DC J 81 " ideal model delta sigma weight residual 108.00 111.37 -3.37 7.00e-01 2.04e+00 2.31e+01 angle pdb=" O4' DC I 81 " pdb=" C4' DC I 81 " pdb=" C3' DC I 81 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.31e+01 ... (remaining 31250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 9259 35.93 - 71.85: 2355 71.85 - 107.78: 33 107.78 - 143.71: 3 143.71 - 179.63: 8 Dihedral angle restraints: 11658 sinusoidal: 8046 harmonic: 3612 Sorted by residual: dihedral pdb=" C4' DC J 159 " pdb=" C3' DC J 159 " pdb=" O3' DC J 159 " pdb=" P DT J 160 " ideal model delta sinusoidal sigma weight residual 220.00 40.37 179.63 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 58 " pdb=" C3' DT J 58 " pdb=" O3' DT J 58 " pdb=" P DA J 59 " ideal model delta sinusoidal sigma weight residual -140.00 36.16 -176.16 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I 118 " pdb=" C3' DT I 118 " pdb=" O3' DT I 118 " pdb=" P DT I 119 " ideal model delta sinusoidal sigma weight residual -140.00 35.42 -175.42 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 11655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2613 0.051 - 0.102: 795 0.102 - 0.153: 131 0.153 - 0.204: 19 0.204 - 0.255: 3 Chirality restraints: 3561 Sorted by residual: chirality pdb=" CB THR N 115 " pdb=" CA THR N 115 " pdb=" OG1 THR N 115 " pdb=" CG2 THR N 115 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" P DC I 151 " pdb=" OP1 DC I 151 " pdb=" OP2 DC I 151 " pdb=" O5' DC I 151 " both_signs ideal model delta sigma weight residual True 2.34 -2.56 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASN G 110 " pdb=" N ASN G 110 " pdb=" C ASN G 110 " pdb=" CB ASN G 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 3558 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " 0.021 2.00e-02 2.50e+03 2.23e-02 9.91e+00 pdb=" CG TYR D 83 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " -0.022 2.00e-02 2.50e+03 2.12e-02 9.02e+00 pdb=" CG TYR B 88 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 64 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C ASN B 64 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN B 64 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL B 65 " -0.016 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 80 2.55 - 3.14: 15356 3.14 - 3.73: 38934 3.73 - 4.31: 49401 4.31 - 4.90: 70758 Nonbonded interactions: 174529 Sorted by model distance: nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 1.966 3.040 nonbonded pdb=" OG SER M 40 " pdb=" O SER N 87 " model vdw 2.113 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.123 3.040 nonbonded pdb=" NH2 ARG A 72 " pdb=" OP1 DG I 52 " model vdw 2.155 3.120 nonbonded pdb=" O VAL B 70 " pdb=" OG1 THR B 73 " model vdw 2.165 3.040 ... (remaining 174524 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' and resid 39 through 133) selection = (chain 'O' and resid 39 through 133) } ncs_group { reference = (chain 'B' and resid 25 through 93) selection = (chain 'F' and resid 25 through 93) selection = chain 'L' selection = (chain 'P' and resid 25 through 93) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 117) selection = chain 'M' } ncs_group { reference = (chain 'D' and resid 34 through 123) selection = chain 'H' selection = (chain 'N' and resid 34 through 123) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.920 Find NCS groups from input model: 0.240 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 21551 Z= 0.531 Angle : 0.886 10.253 31255 Z= 0.735 Chirality : 0.049 0.255 3561 Planarity : 0.006 0.036 2220 Dihedral : 29.357 179.633 9328 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: 1.03 (0.21), residues: 1219 helix: 1.06 (0.15), residues: 918 sheet: None (None), residues: 0 loop : -0.27 (0.30), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 134 TYR 0.055 0.003 TYR D 83 PHE 0.037 0.003 PHE N 65 HIS 0.016 0.003 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.53 (21551) covalent geometry : angle 0.88620 / 0.73 (31255) hydrogen bonds : bond 0.10958 / 7.42 ( 1312) hydrogen bonds : angle 4.51121 / 3.26 ( 3284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PRO cc_start: 0.7798 (Cg_exo) cc_final: 0.7595 (Cg_endo) REVERT: A 61 LEU cc_start: 0.8725 (mt) cc_final: 0.8175 (mp) REVERT: A 84 PHE cc_start: 0.7753 (m-80) cc_final: 0.7509 (m-10) REVERT: A 89 VAL cc_start: 0.9378 (t) cc_final: 0.9170 (p) REVERT: A 92 LEU cc_start: 0.9424 (mt) cc_final: 0.8843 (mt) REVERT: A 93 GLN cc_start: 0.8689 (tt0) cc_final: 0.8324 (tp40) REVERT: A 108 ASN cc_start: 0.8749 (t0) cc_final: 0.8122 (t0) REVERT: B 90 LEU cc_start: 0.9103 (mt) cc_final: 0.8697 (mp) REVERT: B 96 THR cc_start: 0.8661 (p) cc_final: 0.8297 (t) REVERT: C 25 PHE cc_start: 0.8607 (m-80) cc_final: 0.8381 (m-10) REVERT: C 26 PRO cc_start: 0.8556 (Cg_endo) cc_final: 0.8307 (Cg_exo) REVERT: C 78 ILE cc_start: 0.8793 (mm) cc_final: 0.8589 (mm) REVERT: C 91 GLU cc_start: 0.8521 (pm20) cc_final: 0.8174 (pp20) REVERT: C 110 ASN cc_start: 0.8874 (t0) cc_final: 0.8387 (t0) REVERT: D 34 LYS cc_start: 0.7417 (tptp) cc_final: 0.7059 (tppt) REVERT: D 42 TYR cc_start: 0.7662 (t80) cc_final: 0.7372 (t80) REVERT: D 100 LEU cc_start: 0.9272 (mp) cc_final: 0.8717 (mm) REVERT: E 60 LEU cc_start: 0.9028 (mt) cc_final: 0.8488 (mp) REVERT: E 93 GLN cc_start: 0.9291 (tt0) cc_final: 0.8205 (tp-100) REVERT: E 101 VAL cc_start: 0.9409 (m) cc_final: 0.9156 (p) REVERT: E 106 ASP cc_start: 0.8221 (m-30) cc_final: 0.7938 (m-30) REVERT: E 107 THR cc_start: 0.9172 (m) cc_final: 0.8616 (p) REVERT: F 25 ASN cc_start: 0.7342 (m-40) cc_final: 0.6497 (m-40) REVERT: F 49 LEU cc_start: 0.7418 (mp) cc_final: 0.6823 (mt) REVERT: F 59 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8389 (tttt) REVERT: F 85 ASP cc_start: 0.8698 (m-30) cc_final: 0.8139 (m-30) REVERT: G 35 ARG cc_start: 0.7430 (mtm180) cc_final: 0.7185 (ptp90) REVERT: H 37 TYR cc_start: 0.8047 (m-80) cc_final: 0.7624 (m-80) REVERT: H 42 TYR cc_start: 0.7126 (t80) cc_final: 0.6857 (t80) REVERT: H 45 LEU cc_start: 0.7677 (tp) cc_final: 0.7385 (tp) REVERT: H 57 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7832 (mmmt) REVERT: H 59 MET cc_start: 0.8299 (tpp) cc_final: 0.7818 (mmm) REVERT: H 61 ILE cc_start: 0.9130 (mt) cc_final: 0.8748 (mm) REVERT: H 65 PHE cc_start: 0.8710 (t80) cc_final: 0.8290 (t80) REVERT: H 68 ASP cc_start: 0.6642 (t0) cc_final: 0.5851 (t0) REVERT: H 71 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6787 (mt-10) REVERT: H 101 LEU cc_start: 0.8643 (mp) cc_final: 0.8383 (mt) REVERT: L 30 THR cc_start: 0.7324 (p) cc_final: 0.6905 (t) REVERT: L 86 VAL cc_start: 0.4849 (t) cc_final: 0.4545 (t) REVERT: L 87 VAL cc_start: 0.7019 (t) cc_final: 0.6548 (p) REVERT: L 88 TYR cc_start: 0.2709 (m-10) cc_final: 0.2143 (m-10) REVERT: N 41 VAL cc_start: 0.8862 (t) cc_final: 0.8607 (t) REVERT: N 54 ILE cc_start: 0.6872 (tt) cc_final: 0.6551 (pt) REVERT: N 62 MET cc_start: 0.7794 (mmm) cc_final: 0.7351 (mmp) REVERT: N 68 ASP cc_start: 0.7005 (t70) cc_final: 0.6660 (t0) REVERT: O 61 LEU cc_start: 0.8037 (mt) cc_final: 0.7543 (mt) REVERT: O 74 ILE cc_start: 0.8046 (tp) cc_final: 0.7791 (mm) REVERT: O 76 GLN cc_start: 0.8229 (tt0) cc_final: 0.7906 (tp40) REVERT: O 92 LEU cc_start: 0.8473 (mm) cc_final: 0.8143 (mm) REVERT: O 103 LEU cc_start: 0.8743 (tp) cc_final: 0.8488 (tt) REVERT: P 93 GLN cc_start: 0.8772 (tt0) cc_final: 0.8447 (tm-30) outliers start: 0 outliers final: 0 residues processed: 592 average time/residue: 0.1626 time to fit residues: 137.7406 Evaluate side-chains 378 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 50.0000 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 24 GLN D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN M 68 ASN ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 HIS P 25 ASN P 64 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.085772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.063465 restraints weight = 125080.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.064933 restraints weight = 64905.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.065928 restraints weight = 42150.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.066527 restraints weight = 32360.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.066931 restraints weight = 27596.023| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 19 (25 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21551 Z= 0.243 Angle : 0.781 10.395 31255 Z= 0.449 Chirality : 0.048 0.343 3561 Planarity : 0.006 0.077 2220 Dihedral : 32.322 179.980 6852 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.67 % Allowed : 6.31 % Favored : 93.02 % 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: 1.47 (0.22), residues: 1219 helix: 1.37 (0.16), residues: 923 sheet: None (None), residues: 0 loop : -0.08 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 52 TYR 0.048 0.003 TYR B 88 PHE 0.026 0.003 PHE O 67 HIS 0.011 0.003 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.24 (21551) covalent geometry : angle 0.78112 / 0.45 (31255) hydrogen bonds : bond 0.07734 / 5.19 ( 1312) hydrogen bonds : angle 3.99275 / 2.92 ( 3284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 425 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9000 (mt) cc_final: 0.8679 (mp) REVERT: A 84 PHE cc_start: 0.8482 (m-80) cc_final: 0.8207 (m-10) REVERT: A 93 GLN cc_start: 0.9324 (tt0) cc_final: 0.8527 (tp40) REVERT: A 97 GLU cc_start: 0.8159 (pt0) cc_final: 0.7940 (pt0) REVERT: B 68 ASP cc_start: 0.8858 (m-30) cc_final: 0.8632 (m-30) REVERT: B 88 TYR cc_start: 0.8552 (m-10) cc_final: 0.8274 (m-80) REVERT: B 98 TYR cc_start: 0.8504 (m-10) cc_final: 0.8214 (m-10) REVERT: C 35 ARG cc_start: 0.9010 (mtt90) cc_final: 0.8570 (mmt180) REVERT: C 39 TYR cc_start: 0.9098 (m-80) cc_final: 0.7883 (m-80) REVERT: C 110 ASN cc_start: 0.9129 (t0) cc_final: 0.8714 (m110) REVERT: D 34 LYS cc_start: 0.7506 (tptp) cc_final: 0.6314 (mmtt) REVERT: D 44 VAL cc_start: 0.9342 (t) cc_final: 0.8970 (p) REVERT: D 68 ASP cc_start: 0.8461 (t70) cc_final: 0.8099 (t0) REVERT: D 89 ILE cc_start: 0.8912 (mt) cc_final: 0.8378 (tt) REVERT: D 108 LYS cc_start: 0.9097 (mttm) cc_final: 0.8799 (mtpt) REVERT: E 46 VAL cc_start: 0.8213 (t) cc_final: 0.7739 (t) REVERT: E 50 GLU cc_start: 0.8096 (mp0) cc_final: 0.7853 (mm-30) REVERT: E 54 TYR cc_start: 0.8210 (m-10) cc_final: 0.6385 (m-80) REVERT: E 67 PHE cc_start: 0.7813 (t80) cc_final: 0.7491 (t80) REVERT: F 44 LYS cc_start: 0.8619 (ttpp) cc_final: 0.7988 (mtpt) REVERT: F 59 LYS cc_start: 0.8338 (ttpt) cc_final: 0.8014 (tttt) REVERT: F 60 VAL cc_start: 0.9246 (t) cc_final: 0.7645 (t) REVERT: F 88 TYR cc_start: 0.8576 (m-80) cc_final: 0.8268 (m-80) REVERT: G 38 ASN cc_start: 0.7931 (m110) cc_final: 0.7517 (t0) REVERT: G 90 ASP cc_start: 0.8360 (t70) cc_final: 0.8002 (t0) REVERT: H 37 TYR cc_start: 0.8923 (m-80) cc_final: 0.8622 (m-80) REVERT: H 61 ILE cc_start: 0.8916 (mt) cc_final: 0.8681 (mm) REVERT: H 65 PHE cc_start: 0.9088 (t80) cc_final: 0.8549 (t80) REVERT: H 68 ASP cc_start: 0.8334 (t0) cc_final: 0.7401 (t0) REVERT: K 107 THR cc_start: 0.9230 (p) cc_final: 0.9000 (p) REVERT: M 64 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8236 (tm-30) REVERT: M 84 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8551 (tm-30) REVERT: N 68 ASP cc_start: 0.8631 (t70) cc_final: 0.8313 (t0) REVERT: N 71 GLU cc_start: 0.8840 (pp20) cc_final: 0.8390 (pp20) REVERT: O 60 LEU cc_start: 0.5573 (mp) cc_final: 0.4154 (mp) REVERT: O 61 LEU cc_start: 0.8700 (mt) cc_final: 0.7861 (mp) REVERT: O 76 GLN cc_start: 0.9234 (tt0) cc_final: 0.8784 (tp40) REVERT: O 96 CYS cc_start: 0.9464 (m) cc_final: 0.9198 (m) REVERT: O 120 MET cc_start: 0.8108 (ttp) cc_final: 0.7874 (ttm) REVERT: O 123 ASP cc_start: 0.9396 (m-30) cc_final: 0.9150 (m-30) REVERT: P 57 VAL cc_start: 0.9287 (t) cc_final: 0.9083 (p) REVERT: P 84 MET cc_start: 0.7073 (tpp) cc_final: 0.6679 (tpp) REVERT: P 93 GLN cc_start: 0.8587 (tt0) cc_final: 0.8340 (tm-30) outliers start: 7 outliers final: 2 residues processed: 428 average time/residue: 0.1284 time to fit residues: 83.7685 Evaluate side-chains 313 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 311 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 107 optimal weight: 50.0000 chunk 94 optimal weight: 50.0000 chunk 26 optimal weight: 0.9990 chunk 90 optimal weight: 50.0000 chunk 122 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 97 optimal weight: 50.0000 chunk 121 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 93 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.077338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.055546 restraints weight = 121427.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.056961 restraints weight = 63046.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057450 restraints weight = 37500.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.057634 restraints weight = 33369.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057722 restraints weight = 30316.818| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 21551 Z= 0.248 Angle : 0.762 11.921 31255 Z= 0.439 Chirality : 0.047 0.332 3561 Planarity : 0.006 0.063 2220 Dihedral : 32.737 179.184 6852 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.48 % Allowed : 6.12 % Favored : 93.40 % 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: 1.31 (0.22), residues: 1219 helix: 1.25 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -0.14 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 92 TYR 0.035 0.003 TYR B 88 PHE 0.020 0.003 PHE D 65 HIS 0.009 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.25 (21551) covalent geometry : angle 0.76237 / 0.44 (31255) hydrogen bonds : bond 0.07346 / 4.87 ( 1312) hydrogen bonds : angle 3.96284 / 2.90 ( 3284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 388 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8788 (tp40) cc_final: 0.8553 (tp40) REVERT: A 82 LEU cc_start: 0.7907 (mt) cc_final: 0.7704 (mt) REVERT: A 84 PHE cc_start: 0.8427 (m-80) cc_final: 0.8178 (m-10) REVERT: A 93 GLN cc_start: 0.9319 (tt0) cc_final: 0.8533 (tp40) REVERT: A 94 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7962 (tp30) REVERT: B 67 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7815 (tpp80) REVERT: B 74 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7900 (tm-30) REVERT: B 88 TYR cc_start: 0.8407 (m-10) cc_final: 0.8043 (m-10) REVERT: C 56 GLU cc_start: 0.8875 (tt0) cc_final: 0.8372 (tt0) REVERT: C 110 ASN cc_start: 0.9106 (t0) cc_final: 0.8735 (m110) REVERT: D 44 VAL cc_start: 0.9455 (t) cc_final: 0.9077 (p) REVERT: D 68 ASP cc_start: 0.8568 (t70) cc_final: 0.8337 (t0) REVERT: D 82 HIS cc_start: 0.8538 (t-90) cc_final: 0.8207 (t70) REVERT: D 108 LYS cc_start: 0.9065 (mttm) cc_final: 0.8799 (mtpt) REVERT: E 105 GLU cc_start: 0.7975 (pp20) cc_final: 0.7667 (pp20) REVERT: E 106 ASP cc_start: 0.8829 (m-30) cc_final: 0.8538 (m-30) REVERT: F 59 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8223 (tttt) REVERT: F 60 VAL cc_start: 0.9221 (t) cc_final: 0.8830 (t) REVERT: F 88 TYR cc_start: 0.8563 (m-10) cc_final: 0.8349 (m-80) REVERT: H 68 ASP cc_start: 0.8564 (t0) cc_final: 0.7859 (t0) REVERT: H 87 SER cc_start: 0.7995 (m) cc_final: 0.7753 (p) REVERT: H 94 ILE cc_start: 0.9538 (mm) cc_final: 0.9323 (mm) REVERT: H 112 SER cc_start: 0.9162 (t) cc_final: 0.8801 (p) REVERT: L 62 LEU cc_start: 0.9752 (mm) cc_final: 0.9488 (mm) REVERT: M 25 PHE cc_start: 0.7612 (m-10) cc_final: 0.7192 (m-10) REVERT: M 58 LEU cc_start: 0.8973 (mp) cc_final: 0.8689 (pp) REVERT: M 64 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8359 (tm-30) REVERT: M 76 THR cc_start: 0.8370 (m) cc_final: 0.8111 (p) REVERT: M 84 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8670 (tm-30) REVERT: N 68 ASP cc_start: 0.8655 (t70) cc_final: 0.8297 (t0) REVERT: N 71 GLU cc_start: 0.8679 (pp20) cc_final: 0.8269 (pp20) REVERT: O 61 LEU cc_start: 0.8638 (mt) cc_final: 0.7473 (mp) REVERT: O 65 LEU cc_start: 0.8239 (tp) cc_final: 0.7977 (tp) REVERT: O 76 GLN cc_start: 0.9295 (tt0) cc_final: 0.8796 (tp40) REVERT: O 90 MET cc_start: 0.9152 (ptp) cc_final: 0.8935 (ptp) REVERT: O 96 CYS cc_start: 0.9446 (m) cc_final: 0.9064 (m) REVERT: P 93 GLN cc_start: 0.8605 (tt0) cc_final: 0.8158 (tm-30) outliers start: 5 outliers final: 2 residues processed: 389 average time/residue: 0.1276 time to fit residues: 77.8016 Evaluate side-chains 297 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 295 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 134 optimal weight: 6.9990 chunk 87 optimal weight: 50.0000 chunk 78 optimal weight: 40.0000 chunk 123 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 110 optimal weight: 40.0000 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 75 optimal weight: 40.0000 chunk 115 optimal weight: 30.0000 chunk 32 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 110 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN P 64 ASN P 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.076773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.054824 restraints weight = 116739.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.056332 restraints weight = 56911.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.057310 restraints weight = 35829.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057927 restraints weight = 26721.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.058268 restraints weight = 22445.694| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21551 Z= 0.181 Angle : 0.698 9.311 31255 Z= 0.406 Chirality : 0.046 0.334 3561 Planarity : 0.005 0.056 2220 Dihedral : 32.830 179.786 6852 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.27 % 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: 1.42 (0.22), residues: 1219 helix: 1.35 (0.16), residues: 928 sheet: None (None), residues: 0 loop : -0.20 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 92 TYR 0.029 0.003 TYR P 88 PHE 0.018 0.002 PHE N 65 HIS 0.007 0.002 HIS M 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (21551) covalent geometry : angle 0.69822 / 0.41 (31255) hydrogen bonds : bond 0.06068 / 4.03 ( 1312) hydrogen bonds : angle 3.71900 / 2.73 ( 3284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8401 (m-80) cc_final: 0.8040 (m-80) REVERT: A 93 GLN cc_start: 0.9289 (tt0) cc_final: 0.8550 (tp40) REVERT: B 45 ARG cc_start: 0.7933 (tpt-90) cc_final: 0.7651 (tpt-90) REVERT: B 63 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8017 (tm-30) REVERT: B 67 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7779 (tpp80) REVERT: B 74 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 88 TYR cc_start: 0.8285 (m-10) cc_final: 0.6859 (m-10) REVERT: C 35 ARG cc_start: 0.8956 (mtt90) cc_final: 0.8582 (mmt180) REVERT: C 56 GLU cc_start: 0.8898 (tt0) cc_final: 0.7840 (tt0) REVERT: C 104 GLN cc_start: 0.8457 (mt0) cc_final: 0.8073 (mt0) REVERT: C 110 ASN cc_start: 0.8898 (t0) cc_final: 0.8667 (m110) REVERT: D 44 VAL cc_start: 0.9449 (t) cc_final: 0.9044 (p) REVERT: D 82 HIS cc_start: 0.8429 (t-90) cc_final: 0.8116 (t70) REVERT: D 89 ILE cc_start: 0.8847 (mt) cc_final: 0.8407 (tt) REVERT: D 100 LEU cc_start: 0.9138 (mm) cc_final: 0.8938 (mm) REVERT: D 108 LYS cc_start: 0.9130 (mttm) cc_final: 0.8899 (mtpt) REVERT: E 54 TYR cc_start: 0.7947 (m-10) cc_final: 0.7270 (m-80) REVERT: E 57 SER cc_start: 0.8872 (t) cc_final: 0.8314 (p) REVERT: E 67 PHE cc_start: 0.8171 (t80) cc_final: 0.7892 (t80) REVERT: E 93 GLN cc_start: 0.8793 (tt0) cc_final: 0.8106 (tm-30) REVERT: E 109 LEU cc_start: 0.9272 (mp) cc_final: 0.8959 (mt) REVERT: F 59 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7950 (tttt) REVERT: F 60 VAL cc_start: 0.9385 (t) cc_final: 0.8388 (t) REVERT: H 37 TYR cc_start: 0.8929 (m-80) cc_final: 0.7887 (m-10) REVERT: H 68 ASP cc_start: 0.8615 (t0) cc_final: 0.7877 (t0) REVERT: H 87 SER cc_start: 0.8220 (m) cc_final: 0.7970 (p) REVERT: H 106 LEU cc_start: 0.9506 (mt) cc_final: 0.8972 (mt) REVERT: H 112 SER cc_start: 0.9146 (t) cc_final: 0.8831 (p) REVERT: L 62 LEU cc_start: 0.9701 (mm) cc_final: 0.9444 (mm) REVERT: L 85 ASP cc_start: 0.5389 (m-30) cc_final: 0.4743 (m-30) REVERT: M 57 TYR cc_start: 0.8466 (t80) cc_final: 0.8262 (t80) REVERT: M 58 LEU cc_start: 0.8999 (mp) cc_final: 0.8728 (pp) REVERT: M 64 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8229 (tm-30) REVERT: M 76 THR cc_start: 0.8397 (m) cc_final: 0.8166 (p) REVERT: M 84 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8594 (tm-30) REVERT: M 107 VAL cc_start: 0.8863 (t) cc_final: 0.8586 (p) REVERT: N 68 ASP cc_start: 0.8681 (t70) cc_final: 0.8259 (t0) REVERT: N 71 GLU cc_start: 0.8647 (pp20) cc_final: 0.8132 (pp20) REVERT: O 41 TYR cc_start: 0.5904 (m-80) cc_final: 0.5560 (m-80) REVERT: O 76 GLN cc_start: 0.9102 (tt0) cc_final: 0.8625 (tp40) REVERT: O 90 MET cc_start: 0.9161 (ptp) cc_final: 0.8954 (ptp) REVERT: O 96 CYS cc_start: 0.9396 (m) cc_final: 0.9013 (m) REVERT: O 105 GLU cc_start: 0.9246 (pt0) cc_final: 0.9017 (pt0) REVERT: P 93 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7981 (tm-30) outliers start: 1 outliers final: 0 residues processed: 391 average time/residue: 0.1228 time to fit residues: 75.3686 Evaluate side-chains 300 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 113 optimal weight: 40.0000 chunk 105 optimal weight: 50.0000 chunk 82 optimal weight: 30.0000 chunk 137 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 75 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN O 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.075624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053542 restraints weight = 117458.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.055017 restraints weight = 57766.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055983 restraints weight = 36353.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.056592 restraints weight = 27093.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.056967 restraints weight = 22755.691| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21551 Z= 0.208 Angle : 0.719 9.105 31255 Z= 0.414 Chirality : 0.046 0.327 3561 Planarity : 0.006 0.051 2220 Dihedral : 32.906 179.759 6852 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.22), residues: 1219 helix: 1.26 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -0.39 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 92 TYR 0.034 0.003 TYR L 88 PHE 0.015 0.002 PHE A 67 HIS 0.010 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.21 (21551) covalent geometry : angle 0.71889 / 0.41 (31255) hydrogen bonds : bond 0.06646 / 4.44 ( 1312) hydrogen bonds : angle 3.84064 / 2.82 ( 3284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8463 (m-80) cc_final: 0.8127 (m-10) REVERT: A 93 GLN cc_start: 0.9327 (tt0) cc_final: 0.8596 (tp40) REVERT: A 110 CYS cc_start: 0.9345 (m) cc_final: 0.9142 (m) REVERT: B 63 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8331 (tm-30) REVERT: B 68 ASP cc_start: 0.9062 (m-30) cc_final: 0.8825 (m-30) REVERT: B 74 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 88 TYR cc_start: 0.8342 (m-10) cc_final: 0.7351 (m-80) REVERT: C 56 GLU cc_start: 0.8868 (tt0) cc_final: 0.7904 (tt0) REVERT: C 110 ASN cc_start: 0.8874 (t0) cc_final: 0.8659 (m110) REVERT: D 44 VAL cc_start: 0.9422 (t) cc_final: 0.9066 (p) REVERT: D 82 HIS cc_start: 0.8411 (t-90) cc_final: 0.8065 (t70) REVERT: D 89 ILE cc_start: 0.8813 (mt) cc_final: 0.8391 (tt) REVERT: D 100 LEU cc_start: 0.9187 (mm) cc_final: 0.8896 (mm) REVERT: D 108 LYS cc_start: 0.9217 (mttm) cc_final: 0.8908 (mtpt) REVERT: E 54 TYR cc_start: 0.8056 (m-10) cc_final: 0.7354 (m-80) REVERT: E 57 SER cc_start: 0.8956 (t) cc_final: 0.8711 (p) REVERT: E 107 THR cc_start: 0.9286 (m) cc_final: 0.9061 (m) REVERT: E 109 LEU cc_start: 0.9276 (mp) cc_final: 0.8699 (mt) REVERT: F 59 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8100 (tttt) REVERT: F 60 VAL cc_start: 0.9344 (t) cc_final: 0.8301 (t) REVERT: F 88 TYR cc_start: 0.8513 (m-10) cc_final: 0.8266 (m-10) REVERT: G 38 ASN cc_start: 0.8677 (m110) cc_final: 0.8449 (m110) REVERT: H 54 ILE cc_start: 0.8535 (mp) cc_final: 0.8290 (mp) REVERT: H 59 MET cc_start: 0.9241 (tpp) cc_final: 0.8972 (tpp) REVERT: H 68 ASP cc_start: 0.8678 (t0) cc_final: 0.7958 (t0) REVERT: H 87 SER cc_start: 0.8386 (m) cc_final: 0.8109 (p) REVERT: H 94 ILE cc_start: 0.9123 (mm) cc_final: 0.8904 (mm) REVERT: H 112 SER cc_start: 0.9128 (t) cc_final: 0.8723 (p) REVERT: K 103 LEU cc_start: 0.9353 (mt) cc_final: 0.9040 (mt) REVERT: K 107 THR cc_start: 0.9319 (p) cc_final: 0.8359 (p) REVERT: K 123 ASP cc_start: 0.8618 (m-30) cc_final: 0.7493 (t0) REVERT: L 88 TYR cc_start: 0.5269 (m-80) cc_final: 0.5067 (m-10) REVERT: M 25 PHE cc_start: 0.7541 (m-10) cc_final: 0.6856 (m-10) REVERT: M 56 GLU cc_start: 0.8750 (pt0) cc_final: 0.8415 (tt0) REVERT: M 58 LEU cc_start: 0.9105 (mp) cc_final: 0.8841 (pp) REVERT: M 64 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8284 (tm-30) REVERT: M 76 THR cc_start: 0.8403 (m) cc_final: 0.8183 (p) REVERT: M 84 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8561 (tm-30) REVERT: M 107 VAL cc_start: 0.9090 (t) cc_final: 0.8824 (p) REVERT: N 68 ASP cc_start: 0.8905 (t0) cc_final: 0.8358 (t0) REVERT: N 71 GLU cc_start: 0.8647 (pp20) cc_final: 0.8303 (pp20) REVERT: N 76 GLU cc_start: 0.7277 (tp30) cc_final: 0.6945 (tp30) REVERT: O 41 TYR cc_start: 0.5925 (m-80) cc_final: 0.5512 (m-80) REVERT: O 53 ARG cc_start: 0.9372 (tpp-160) cc_final: 0.9154 (tmt-80) REVERT: O 76 GLN cc_start: 0.9062 (tt0) cc_final: 0.8622 (tp40) REVERT: O 80 THR cc_start: 0.7183 (p) cc_final: 0.6900 (t) REVERT: O 96 CYS cc_start: 0.9464 (m) cc_final: 0.9066 (m) REVERT: O 101 VAL cc_start: 0.9394 (m) cc_final: 0.8895 (p) REVERT: O 105 GLU cc_start: 0.9277 (pt0) cc_final: 0.9033 (pt0) REVERT: O 120 MET cc_start: 0.8620 (ttt) cc_final: 0.8369 (ttt) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.1223 time to fit residues: 72.2742 Evaluate side-chains 302 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 110 optimal weight: 40.0000 chunk 156 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 93 optimal weight: 50.0000 chunk 120 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN P 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.076430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.054363 restraints weight = 120622.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055747 restraints weight = 64174.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.056182 restraints weight = 37761.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.056590 restraints weight = 32665.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.056624 restraints weight = 29275.961| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21551 Z= 0.181 Angle : 0.705 8.126 31255 Z= 0.406 Chirality : 0.046 0.328 3561 Planarity : 0.006 0.095 2220 Dihedral : 32.968 178.965 6852 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.19 % Allowed : 2.77 % Favored : 97.04 % 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: 1.29 (0.22), residues: 1219 helix: 1.32 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -0.50 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 92 TYR 0.038 0.002 TYR C 57 PHE 0.015 0.002 PHE A 67 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 (21551) covalent geometry : angle 0.70465 / 0.41 (31255) hydrogen bonds : bond 0.05951 / 3.97 ( 1312) hydrogen bonds : angle 3.71975 / 2.75 ( 3284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 381 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8393 (m-80) cc_final: 0.8066 (m-80) REVERT: A 93 GLN cc_start: 0.9305 (tt0) cc_final: 0.8591 (tp40) REVERT: A 110 CYS cc_start: 0.9344 (m) cc_final: 0.9116 (m) REVERT: B 45 ARG cc_start: 0.8151 (tpt-90) cc_final: 0.7718 (tpt-90) REVERT: B 63 GLU cc_start: 0.8786 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 67 ARG cc_start: 0.8715 (tpp80) cc_final: 0.8219 (tpp80) REVERT: B 68 ASP cc_start: 0.9122 (m-30) cc_final: 0.8825 (m-30) REVERT: B 74 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 88 TYR cc_start: 0.7741 (m-10) cc_final: 0.7252 (m-10) REVERT: C 56 GLU cc_start: 0.8900 (tt0) cc_final: 0.7924 (tt0) REVERT: C 104 GLN cc_start: 0.8733 (mt0) cc_final: 0.8260 (mt0) REVERT: C 110 ASN cc_start: 0.8959 (t0) cc_final: 0.8720 (m110) REVERT: C 111 ILE cc_start: 0.8949 (mp) cc_final: 0.8608 (mt) REVERT: D 44 VAL cc_start: 0.9420 (t) cc_final: 0.9057 (p) REVERT: D 82 HIS cc_start: 0.8410 (t-90) cc_final: 0.8132 (t70) REVERT: D 89 ILE cc_start: 0.8763 (mt) cc_final: 0.8358 (tt) REVERT: D 96 THR cc_start: 0.9491 (t) cc_final: 0.9218 (p) REVERT: D 100 LEU cc_start: 0.9195 (mm) cc_final: 0.8951 (mm) REVERT: D 108 LYS cc_start: 0.9220 (mttm) cc_final: 0.8987 (mtpt) REVERT: E 54 TYR cc_start: 0.8076 (m-10) cc_final: 0.7272 (m-80) REVERT: E 57 SER cc_start: 0.8891 (t) cc_final: 0.8680 (p) REVERT: E 59 GLU cc_start: 0.8118 (pm20) cc_final: 0.7746 (pm20) REVERT: E 90 MET cc_start: 0.8990 (mmm) cc_final: 0.8421 (tmm) REVERT: E 93 GLN cc_start: 0.8704 (tt0) cc_final: 0.8037 (tt0) REVERT: F 27 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8376 (mp10) REVERT: F 44 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8396 (mtpt) REVERT: F 60 VAL cc_start: 0.9195 (t) cc_final: 0.8737 (t) REVERT: F 88 TYR cc_start: 0.8423 (m-10) cc_final: 0.8190 (m-10) REVERT: G 38 ASN cc_start: 0.8848 (m110) cc_final: 0.8092 (t0) REVERT: G 68 ASN cc_start: 0.9174 (m110) cc_final: 0.8887 (m-40) REVERT: H 37 TYR cc_start: 0.8851 (m-80) cc_final: 0.7772 (m-10) REVERT: H 68 ASP cc_start: 0.8670 (t0) cc_final: 0.7987 (t0) REVERT: H 94 ILE cc_start: 0.9105 (mm) cc_final: 0.8888 (mm) REVERT: H 112 SER cc_start: 0.9127 (t) cc_final: 0.8879 (p) REVERT: H 113 GLU cc_start: 0.8554 (mp0) cc_final: 0.8025 (mp0) REVERT: K 63 ARG cc_start: 0.4903 (ttm170) cc_final: 0.4239 (ptp-110) REVERT: K 90 MET cc_start: 0.8531 (mmp) cc_final: 0.8264 (mmp) REVERT: K 103 LEU cc_start: 0.9250 (mt) cc_final: 0.8982 (mt) REVERT: K 107 THR cc_start: 0.9249 (p) cc_final: 0.8458 (p) REVERT: K 123 ASP cc_start: 0.8592 (m-30) cc_final: 0.7489 (t0) REVERT: M 25 PHE cc_start: 0.7649 (m-10) cc_final: 0.7092 (m-10) REVERT: M 49 VAL cc_start: 0.7647 (t) cc_final: 0.7366 (p) REVERT: M 56 GLU cc_start: 0.8764 (pt0) cc_final: 0.8316 (tt0) REVERT: M 58 LEU cc_start: 0.9302 (mp) cc_final: 0.8819 (pp) REVERT: M 64 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8228 (tm-30) REVERT: M 76 THR cc_start: 0.8368 (m) cc_final: 0.8118 (p) REVERT: M 84 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8554 (tm-30) REVERT: M 107 VAL cc_start: 0.9134 (t) cc_final: 0.8886 (p) REVERT: N 68 ASP cc_start: 0.8764 (t0) cc_final: 0.8307 (t0) REVERT: N 71 GLU cc_start: 0.8649 (pp20) cc_final: 0.8285 (pp20) REVERT: O 76 GLN cc_start: 0.9026 (tt0) cc_final: 0.8605 (tp40) REVERT: O 80 THR cc_start: 0.7181 (p) cc_final: 0.6899 (t) REVERT: O 96 CYS cc_start: 0.9561 (m) cc_final: 0.9144 (m) REVERT: O 101 VAL cc_start: 0.9425 (m) cc_final: 0.8864 (p) REVERT: O 105 GLU cc_start: 0.9246 (pt0) cc_final: 0.8976 (pt0) outliers start: 2 outliers final: 0 residues processed: 381 average time/residue: 0.1215 time to fit residues: 72.6173 Evaluate side-chains 295 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 57 optimal weight: 0.9990 chunk 75 optimal weight: 40.0000 chunk 131 optimal weight: 5.9990 chunk 133 optimal weight: 40.0000 chunk 83 optimal weight: 40.0000 chunk 121 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 50.0000 chunk 91 optimal weight: 40.0000 chunk 58 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 24 GLN D 47 GLN D 95 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.074462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.052571 restraints weight = 117774.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054014 restraints weight = 58198.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.054953 restraints weight = 36769.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055548 restraints weight = 27549.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.055911 restraints weight = 23194.499| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21551 Z= 0.218 Angle : 0.742 8.549 31255 Z= 0.424 Chirality : 0.047 0.321 3561 Planarity : 0.006 0.117 2220 Dihedral : 33.085 177.949 6852 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.80 % 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: 0.89 (0.22), residues: 1219 helix: 1.06 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -0.74 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 92 TYR 0.056 0.003 TYR B 88 PHE 0.021 0.002 PHE F 61 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.22 (21551) covalent geometry : angle 0.74190 / 0.42 (31255) hydrogen bonds : bond 0.06988 / 4.67 ( 1312) hydrogen bonds : angle 3.91157 / 2.85 ( 3284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8432 (m-80) cc_final: 0.8088 (m-80) REVERT: A 93 GLN cc_start: 0.9309 (tt0) cc_final: 0.8585 (tp40) REVERT: A 110 CYS cc_start: 0.9329 (m) cc_final: 0.9083 (m) REVERT: B 45 ARG cc_start: 0.8154 (tpt-90) cc_final: 0.7870 (tpt-90) REVERT: B 63 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8444 (tm-30) REVERT: B 74 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 85 ASP cc_start: 0.8752 (m-30) cc_final: 0.8129 (m-30) REVERT: C 56 GLU cc_start: 0.8895 (tt0) cc_final: 0.7904 (tt0) REVERT: C 104 GLN cc_start: 0.8658 (mt0) cc_final: 0.8203 (mt0) REVERT: D 42 TYR cc_start: 0.8657 (t80) cc_final: 0.8414 (t80) REVERT: D 44 VAL cc_start: 0.9463 (t) cc_final: 0.9132 (p) REVERT: D 89 ILE cc_start: 0.8826 (mt) cc_final: 0.8444 (tt) REVERT: D 96 THR cc_start: 0.9371 (t) cc_final: 0.9127 (p) REVERT: E 54 TYR cc_start: 0.8092 (m-10) cc_final: 0.7451 (m-80) REVERT: E 57 SER cc_start: 0.8706 (t) cc_final: 0.8486 (p) REVERT: E 90 MET cc_start: 0.9053 (mmm) cc_final: 0.8796 (mmm) REVERT: E 93 GLN cc_start: 0.8700 (tt0) cc_final: 0.8459 (tt0) REVERT: F 39 ARG cc_start: 0.8940 (mmt90) cc_final: 0.8701 (mmm-85) REVERT: F 60 VAL cc_start: 0.9156 (t) cc_final: 0.8719 (t) REVERT: G 38 ASN cc_start: 0.8761 (m110) cc_final: 0.8210 (t0) REVERT: G 68 ASN cc_start: 0.9199 (m110) cc_final: 0.8879 (m-40) REVERT: G 95 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8015 (tmtt) REVERT: H 37 TYR cc_start: 0.8833 (m-80) cc_final: 0.7826 (m-10) REVERT: H 59 MET cc_start: 0.9272 (tpp) cc_final: 0.8875 (tpp) REVERT: H 68 ASP cc_start: 0.8772 (t0) cc_final: 0.7928 (t0) REVERT: H 112 SER cc_start: 0.9105 (t) cc_final: 0.8670 (p) REVERT: K 103 LEU cc_start: 0.9289 (mt) cc_final: 0.9018 (mt) REVERT: K 107 THR cc_start: 0.9214 (p) cc_final: 0.8353 (p) REVERT: K 123 ASP cc_start: 0.8606 (m-30) cc_final: 0.7442 (t0) REVERT: M 25 PHE cc_start: 0.7611 (m-10) cc_final: 0.7110 (m-10) REVERT: M 49 VAL cc_start: 0.7930 (t) cc_final: 0.7610 (p) REVERT: M 56 GLU cc_start: 0.8802 (pt0) cc_final: 0.8267 (tt0) REVERT: M 58 LEU cc_start: 0.9218 (mp) cc_final: 0.8715 (pp) REVERT: M 64 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8231 (tm-30) REVERT: M 84 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8524 (tm-30) REVERT: M 107 VAL cc_start: 0.9031 (t) cc_final: 0.8758 (p) REVERT: N 54 ILE cc_start: 0.7026 (pt) cc_final: 0.6780 (pt) REVERT: N 68 ASP cc_start: 0.8877 (t0) cc_final: 0.8307 (t0) REVERT: N 71 GLU cc_start: 0.8652 (pp20) cc_final: 0.8247 (pp20) REVERT: N 102 LEU cc_start: 0.8140 (mp) cc_final: 0.7644 (tp) REVERT: N 106 LEU cc_start: 0.9302 (mt) cc_final: 0.9099 (mt) REVERT: O 76 GLN cc_start: 0.8756 (tt0) cc_final: 0.8289 (tp40) REVERT: O 96 CYS cc_start: 0.9391 (m) cc_final: 0.9143 (m) REVERT: O 101 VAL cc_start: 0.9462 (m) cc_final: 0.8950 (p) REVERT: O 105 GLU cc_start: 0.9263 (pt0) cc_final: 0.8999 (pt0) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.1226 time to fit residues: 69.5128 Evaluate side-chains 292 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 12 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 97 optimal weight: 50.0000 chunk 124 optimal weight: 0.9990 chunk 148 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 71 optimal weight: 50.0000 chunk 26 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 95 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.076562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.054399 restraints weight = 116309.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.055917 restraints weight = 55952.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.056900 restraints weight = 35211.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.057535 restraints weight = 26402.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.057830 restraints weight = 22216.231| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21551 Z= 0.155 Angle : 0.714 10.325 31255 Z= 0.406 Chirality : 0.047 0.327 3561 Planarity : 0.005 0.053 2220 Dihedral : 33.026 179.058 6852 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.10 % Allowed : 0.86 % Favored : 99.04 % 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: 1.07 (0.23), residues: 1219 helix: 1.21 (0.16), residues: 933 sheet: None (None), residues: 0 loop : -0.82 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 42 TYR 0.029 0.003 TYR C 57 PHE 0.017 0.002 PHE O 67 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.16 (21551) covalent geometry : angle 0.71367 / 0.41 (31255) hydrogen bonds : bond 0.05319 / 3.52 ( 1312) hydrogen bonds : angle 3.67163 / 2.68 ( 3284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8886 (mm) cc_final: 0.8586 (mm) REVERT: A 84 PHE cc_start: 0.8225 (m-80) cc_final: 0.7794 (m-80) REVERT: A 106 ASP cc_start: 0.8930 (m-30) cc_final: 0.8498 (m-30) REVERT: A 110 CYS cc_start: 0.9265 (m) cc_final: 0.8915 (t) REVERT: B 45 ARG cc_start: 0.8178 (tpt-90) cc_final: 0.7790 (tpt-90) REVERT: B 63 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8204 (tm-30) REVERT: B 67 ARG cc_start: 0.8912 (tpp80) cc_final: 0.8254 (tpp80) REVERT: B 74 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 84 MET cc_start: 0.8247 (mmm) cc_final: 0.7692 (tpp) REVERT: B 85 ASP cc_start: 0.8802 (m-30) cc_final: 0.8329 (m-30) REVERT: B 88 TYR cc_start: 0.7090 (m-10) cc_final: 0.6754 (m-10) REVERT: C 35 ARG cc_start: 0.8990 (mtt90) cc_final: 0.8546 (mmt180) REVERT: C 56 GLU cc_start: 0.8853 (tt0) cc_final: 0.8397 (tt0) REVERT: C 57 TYR cc_start: 0.8619 (t80) cc_final: 0.8370 (t80) REVERT: C 110 ASN cc_start: 0.9048 (t0) cc_final: 0.8689 (m110) REVERT: D 44 VAL cc_start: 0.9447 (t) cc_final: 0.9097 (p) REVERT: D 89 ILE cc_start: 0.8530 (mt) cc_final: 0.8082 (tt) REVERT: D 96 THR cc_start: 0.9319 (t) cc_final: 0.9072 (p) REVERT: E 54 TYR cc_start: 0.7842 (m-10) cc_final: 0.7135 (m-80) REVERT: E 57 SER cc_start: 0.8947 (t) cc_final: 0.8604 (p) REVERT: E 59 GLU cc_start: 0.8085 (pm20) cc_final: 0.7776 (pm20) REVERT: E 67 PHE cc_start: 0.8140 (t80) cc_final: 0.7857 (t80) REVERT: E 90 MET cc_start: 0.9015 (mmm) cc_final: 0.8651 (tmm) REVERT: E 107 THR cc_start: 0.9225 (m) cc_final: 0.8972 (p) REVERT: F 27 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8380 (mp10) REVERT: F 44 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8384 (mtpt) REVERT: F 60 VAL cc_start: 0.9366 (t) cc_final: 0.8486 (t) REVERT: G 38 ASN cc_start: 0.8710 (m110) cc_final: 0.7827 (t0) REVERT: G 68 ASN cc_start: 0.9194 (m110) cc_final: 0.8909 (m-40) REVERT: H 37 TYR cc_start: 0.8786 (m-80) cc_final: 0.7791 (m-80) REVERT: H 59 MET cc_start: 0.9192 (tpp) cc_final: 0.8845 (tpp) REVERT: H 68 ASP cc_start: 0.8437 (t0) cc_final: 0.7810 (t0) REVERT: H 113 GLU cc_start: 0.8517 (mp0) cc_final: 0.7943 (mp0) REVERT: K 65 LEU cc_start: 0.7764 (tp) cc_final: 0.7507 (tt) REVERT: K 78 PHE cc_start: 0.7729 (m-80) cc_final: 0.7410 (m-80) REVERT: K 90 MET cc_start: 0.8695 (mmp) cc_final: 0.8398 (mmp) REVERT: K 103 LEU cc_start: 0.9279 (mt) cc_final: 0.9021 (mt) REVERT: K 107 THR cc_start: 0.9175 (p) cc_final: 0.8380 (p) REVERT: K 123 ASP cc_start: 0.8393 (m-30) cc_final: 0.7291 (t0) REVERT: M 49 VAL cc_start: 0.7930 (t) cc_final: 0.7608 (p) REVERT: M 58 LEU cc_start: 0.8886 (mp) cc_final: 0.8484 (pp) REVERT: M 64 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8231 (tm-30) REVERT: N 102 LEU cc_start: 0.8061 (mp) cc_final: 0.7754 (mt) REVERT: O 41 TYR cc_start: 0.5662 (m-80) cc_final: 0.5063 (m-80) REVERT: O 64 LYS cc_start: 0.8361 (pptt) cc_final: 0.8137 (pptt) REVERT: O 65 LEU cc_start: 0.8257 (tp) cc_final: 0.7968 (tp) REVERT: O 68 GLN cc_start: 0.8981 (mt0) cc_final: 0.8767 (mt0) REVERT: O 76 GLN cc_start: 0.8785 (tt0) cc_final: 0.8264 (tp40) REVERT: O 96 CYS cc_start: 0.9438 (m) cc_final: 0.9054 (m) REVERT: O 101 VAL cc_start: 0.9442 (m) cc_final: 0.8892 (p) REVERT: O 105 GLU cc_start: 0.9254 (pt0) cc_final: 0.8962 (pt0) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.1173 time to fit residues: 70.7414 Evaluate side-chains 299 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 118 optimal weight: 40.0000 chunk 101 optimal weight: 50.0000 chunk 21 optimal weight: 6.9990 chunk 97 optimal weight: 50.0000 chunk 163 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 114 optimal weight: 40.0000 chunk 103 optimal weight: 50.0000 chunk 83 optimal weight: 40.0000 chunk 109 optimal weight: 30.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN O 125 GLN P 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.072102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.050339 restraints weight = 124081.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051715 restraints weight = 65094.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.052240 restraints weight = 36963.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.052331 restraints weight = 33756.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052378 restraints weight = 31089.681| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 21551 Z= 0.372 Angle : 0.900 15.555 31255 Z= 0.501 Chirality : 0.054 0.309 3561 Planarity : 0.008 0.087 2220 Dihedral : 33.371 177.449 6852 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -0.19 (0.21), residues: 1219 helix: 0.24 (0.15), residues: 927 sheet: None (None), residues: 0 loop : -0.96 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 35 TYR 0.075 0.005 TYR F 88 PHE 0.029 0.004 PHE B 61 HIS 0.020 0.004 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.37 (21551) covalent geometry : angle 0.89981 / 0.50 (31255) hydrogen bonds : bond 0.11045 / 7.38 ( 1312) hydrogen bonds : angle 4.57025 / 3.35 ( 3284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8389 (m-80) cc_final: 0.7970 (m-10) REVERT: A 110 CYS cc_start: 0.9385 (m) cc_final: 0.9104 (m) REVERT: B 44 LYS cc_start: 0.8126 (tttm) cc_final: 0.7460 (tttt) REVERT: B 45 ARG cc_start: 0.8258 (tpt-90) cc_final: 0.7941 (tpt-90) REVERT: B 52 GLU cc_start: 0.8379 (mp0) cc_final: 0.8090 (mp0) REVERT: B 63 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 74 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 85 ASP cc_start: 0.8490 (m-30) cc_final: 0.8079 (m-30) REVERT: B 98 TYR cc_start: 0.8817 (m-10) cc_final: 0.8538 (m-10) REVERT: C 56 GLU cc_start: 0.8762 (tt0) cc_final: 0.8458 (tt0) REVERT: D 44 VAL cc_start: 0.9559 (t) cc_final: 0.9314 (p) REVERT: D 68 ASP cc_start: 0.8495 (t70) cc_final: 0.8184 (t0) REVERT: D 89 ILE cc_start: 0.8862 (mt) cc_final: 0.8451 (tt) REVERT: E 54 TYR cc_start: 0.8052 (m-10) cc_final: 0.7530 (m-80) REVERT: E 90 MET cc_start: 0.8868 (mmm) cc_final: 0.8445 (mmm) REVERT: E 93 GLN cc_start: 0.8555 (tt0) cc_final: 0.8058 (tt0) REVERT: E 107 THR cc_start: 0.9256 (m) cc_final: 0.9018 (p) REVERT: F 44 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8398 (mtpp) REVERT: F 60 VAL cc_start: 0.9175 (t) cc_final: 0.8695 (t) REVERT: F 79 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6802 (mmtt) REVERT: F 85 ASP cc_start: 0.8371 (m-30) cc_final: 0.8116 (m-30) REVERT: F 88 TYR cc_start: 0.8642 (m-80) cc_final: 0.8241 (m-80) REVERT: G 38 ASN cc_start: 0.8954 (m110) cc_final: 0.8394 (t0) REVERT: G 68 ASN cc_start: 0.9165 (m110) cc_final: 0.8768 (m-40) REVERT: G 95 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8057 (tmtt) REVERT: H 37 TYR cc_start: 0.8920 (m-80) cc_final: 0.8006 (m-10) REVERT: H 113 GLU cc_start: 0.8775 (mp0) cc_final: 0.8431 (mp0) REVERT: K 65 LEU cc_start: 0.7829 (tp) cc_final: 0.7569 (tt) REVERT: K 90 MET cc_start: 0.8662 (mmp) cc_final: 0.8378 (mmp) REVERT: K 97 GLU cc_start: 0.8741 (mp0) cc_final: 0.8541 (mp0) REVERT: K 107 THR cc_start: 0.9190 (p) cc_final: 0.8424 (p) REVERT: K 123 ASP cc_start: 0.8522 (m-30) cc_final: 0.7533 (t0) REVERT: M 25 PHE cc_start: 0.7767 (m-10) cc_final: 0.7137 (m-10) REVERT: M 49 VAL cc_start: 0.7940 (t) cc_final: 0.7564 (p) REVERT: M 56 GLU cc_start: 0.8678 (pt0) cc_final: 0.8302 (tt0) REVERT: M 59 THR cc_start: 0.9379 (m) cc_final: 0.9100 (p) REVERT: M 64 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8294 (tm-30) REVERT: N 71 GLU cc_start: 0.8663 (pp20) cc_final: 0.8226 (pp20) REVERT: N 102 LEU cc_start: 0.8152 (mp) cc_final: 0.7830 (tp) REVERT: O 41 TYR cc_start: 0.6040 (m-80) cc_final: 0.5321 (m-80) REVERT: O 76 GLN cc_start: 0.8747 (tt0) cc_final: 0.8212 (tp40) REVERT: O 96 CYS cc_start: 0.9453 (m) cc_final: 0.9154 (m) REVERT: O 101 VAL cc_start: 0.9525 (m) cc_final: 0.8967 (p) REVERT: O 105 GLU cc_start: 0.9277 (pt0) cc_final: 0.9007 (pt0) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1178 time to fit residues: 64.2326 Evaluate side-chains 278 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 50.0000 chunk 8 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 94 optimal weight: 50.0000 chunk 132 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 141 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.074203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.052278 restraints weight = 118774.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053816 restraints weight = 56375.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.054796 restraints weight = 35136.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055400 restraints weight = 26210.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.055729 restraints weight = 22053.835| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21551 Z= 0.184 Angle : 0.755 9.947 31255 Z= 0.426 Chirality : 0.049 0.300 3561 Planarity : 0.006 0.072 2220 Dihedral : 33.427 178.848 6852 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1219 helix: 0.80 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -0.91 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 92 TYR 0.063 0.003 TYR F 88 PHE 0.019 0.003 PHE F 61 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (21551) covalent geometry : angle 0.75496 / 0.43 (31255) hydrogen bonds : bond 0.06132 / 4.08 ( 1312) hydrogen bonds : angle 3.97705 / 2.91 ( 3284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9016 (mm) cc_final: 0.8686 (mm) REVERT: A 84 PHE cc_start: 0.8249 (m-80) cc_final: 0.7849 (m-10) REVERT: A 101 VAL cc_start: 0.8845 (m) cc_final: 0.8618 (p) REVERT: A 110 CYS cc_start: 0.9329 (m) cc_final: 0.9075 (t) REVERT: A 120 MET cc_start: 0.9169 (mtm) cc_final: 0.8838 (mtp) REVERT: B 44 LYS cc_start: 0.8175 (tttm) cc_final: 0.7511 (tttt) REVERT: B 45 ARG cc_start: 0.8329 (tpt-90) cc_final: 0.7889 (tpt-90) REVERT: B 52 GLU cc_start: 0.8351 (mp0) cc_final: 0.8032 (mp0) REVERT: B 63 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8543 (tm-30) REVERT: B 74 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 35 ARG cc_start: 0.8969 (mtt90) cc_final: 0.8521 (mmt180) REVERT: C 56 GLU cc_start: 0.8808 (tt0) cc_final: 0.8497 (tt0) REVERT: D 44 VAL cc_start: 0.9507 (t) cc_final: 0.9207 (p) REVERT: D 68 ASP cc_start: 0.8501 (t70) cc_final: 0.8174 (t0) REVERT: D 83 TYR cc_start: 0.8195 (t80) cc_final: 0.7871 (t80) REVERT: D 88 THR cc_start: 0.8570 (p) cc_final: 0.8342 (p) REVERT: D 89 ILE cc_start: 0.8768 (mt) cc_final: 0.8430 (tt) REVERT: D 96 THR cc_start: 0.9353 (t) cc_final: 0.9090 (p) REVERT: E 54 TYR cc_start: 0.8386 (m-10) cc_final: 0.7488 (m-80) REVERT: E 93 GLN cc_start: 0.8681 (tt0) cc_final: 0.8027 (tm-30) REVERT: E 94 GLU cc_start: 0.8763 (tt0) cc_final: 0.8435 (tt0) REVERT: E 97 GLU cc_start: 0.8580 (pm20) cc_final: 0.7772 (pm20) REVERT: E 107 THR cc_start: 0.9240 (m) cc_final: 0.8968 (p) REVERT: F 60 VAL cc_start: 0.9391 (t) cc_final: 0.8353 (t) REVERT: F 88 TYR cc_start: 0.8523 (m-80) cc_final: 0.8199 (m-80) REVERT: G 38 ASN cc_start: 0.8911 (m110) cc_final: 0.8401 (t0) REVERT: G 68 ASN cc_start: 0.9180 (m110) cc_final: 0.8837 (m-40) REVERT: G 95 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7833 (tmtt) REVERT: H 37 TYR cc_start: 0.8870 (m-80) cc_final: 0.7850 (m-80) REVERT: H 59 MET cc_start: 0.9269 (tpp) cc_final: 0.8995 (tpp) REVERT: K 65 LEU cc_start: 0.7729 (tp) cc_final: 0.7485 (tt) REVERT: K 78 PHE cc_start: 0.7654 (m-80) cc_final: 0.7287 (m-80) REVERT: K 90 MET cc_start: 0.8648 (mmp) cc_final: 0.8395 (mmp) REVERT: K 97 GLU cc_start: 0.8757 (mp0) cc_final: 0.8547 (mp0) REVERT: K 107 THR cc_start: 0.9167 (p) cc_final: 0.8433 (p) REVERT: K 123 ASP cc_start: 0.8456 (m-30) cc_final: 0.7423 (t0) REVERT: M 25 PHE cc_start: 0.7657 (m-10) cc_final: 0.7156 (m-10) REVERT: M 49 VAL cc_start: 0.7898 (t) cc_final: 0.7585 (p) REVERT: M 56 GLU cc_start: 0.8506 (pt0) cc_final: 0.8170 (tt0) REVERT: M 64 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8292 (tm-30) REVERT: M 84 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8410 (tm-30) REVERT: N 43 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8397 (tptp) REVERT: N 99 ARG cc_start: 0.8538 (ttp-170) cc_final: 0.7773 (mtt180) REVERT: N 102 LEU cc_start: 0.7956 (mp) cc_final: 0.7651 (tp) REVERT: O 41 TYR cc_start: 0.5753 (m-80) cc_final: 0.5248 (m-80) REVERT: O 76 GLN cc_start: 0.8771 (tt0) cc_final: 0.8243 (tp40) REVERT: O 96 CYS cc_start: 0.9436 (m) cc_final: 0.9107 (m) REVERT: O 101 VAL cc_start: 0.9467 (m) cc_final: 0.8947 (p) REVERT: O 105 GLU cc_start: 0.9281 (pt0) cc_final: 0.9003 (pt0) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1175 time to fit residues: 66.2377 Evaluate side-chains 292 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 71 optimal weight: 50.0000 chunk 92 optimal weight: 50.0000 chunk 81 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 103 optimal weight: 50.0000 chunk 153 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 95 optimal weight: 50.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN M 31 HIS P 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.072456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.050594 restraints weight = 124059.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051911 restraints weight = 64237.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052507 restraints weight = 38349.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.052729 restraints weight = 31576.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.052788 restraints weight = 29393.324| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 21551 Z= 0.290 Angle : 0.820 10.908 31255 Z= 0.461 Chirality : 0.051 0.287 3561 Planarity : 0.007 0.077 2220 Dihedral : 33.502 176.340 6852 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 0.15 (0.22), residues: 1219 helix: 0.52 (0.16), residues: 931 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 92 TYR 0.057 0.003 TYR F 88 PHE 0.025 0.003 PHE A 104 HIS 0.014 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.29 (21551) covalent geometry : angle 0.82032 / 0.46 (31255) hydrogen bonds : bond 0.08728 / 5.84 ( 1312) hydrogen bonds : angle 4.27382 / 3.13 ( 3284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2972.91 seconds wall clock time: 52 minutes 12.02 seconds (3132.02 seconds total)