Starting phenix.real_space_refine on Fri Aug 7 04:35:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3f_38880/08_2026/8y3f_38880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3f_38880/08_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_38880/08_2026/8y3f_38880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3f_38880/08_2026/8y3f_38880.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y3f_38880/08_2026/8y3f_38880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3f_38880/08_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-2.2rc3-6140/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: 4.53, per 1000 atoms: 0.22 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: 1.76 Conformation dependent library (CDL) restraints added in 468.7 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: 2.93 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: 3.79 Time building geometry restraints manager: 2.36 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: 29760 2.05 - 4.10: 1399 4.10 - 6.15: 75 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: 0.320 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.590 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- 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= 0.532 Angle : 0.892 10.253 31255 Z= 0.740 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 0.89215 / 0.74 (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 : 0.532 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: A 43 PRO cc_start: 0.7798 (Cg_exo) cc_final: 0.7555 (Cg_endo) REVERT: A 61 LEU cc_start: 0.8725 (mt) cc_final: 0.8183 (mp) REVERT: A 84 PHE cc_start: 0.7753 (m-80) cc_final: 0.7507 (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: 0.8841 (mt) REVERT: A 93 GLN cc_start: 0.8689 (tt0) cc_final: 0.8321 (tp40) REVERT: A 108 ASN cc_start: 0.8749 (t0) cc_final: 0.8145 (t0) REVERT: B 90 LEU cc_start: 0.9103 (mt) cc_final: 0.8696 (mp) REVERT: B 96 THR cc_start: 0.8661 (p) cc_final: 0.8290 (t) REVERT: C 25 PHE cc_start: 0.8607 (m-80) cc_final: 0.8382 (m-10) REVERT: C 26 PRO cc_start: 0.8556 (Cg_endo) cc_final: 0.8314 (Cg_exo) 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: 0.8377 (t0) REVERT: D 34 LYS cc_start: 0.7417 (tptp) cc_final: 0.7024 (tppt) REVERT: D 42 TYR cc_start: 0.7662 (t80) cc_final: 0.7379 (t80) REVERT: D 100 LEU cc_start: 0.9272 (mp) cc_final: 0.8716 (mm) REVERT: E 60 LEU cc_start: 0.9028 (mt) cc_final: 0.8491 (mp) REVERT: E 93 GLN cc_start: 0.9291 (tt0) cc_final: 0.8200 (tp-100) REVERT: E 101 VAL cc_start: 0.9409 (m) cc_final: 0.9155 (p) REVERT: E 106 ASP cc_start: 0.8221 (m-30) cc_final: 0.7936 (m-30) REVERT: E 107 THR cc_start: 0.9172 (m) cc_final: 0.8600 (p) REVERT: F 25 ASN cc_start: 0.7342 (m-40) cc_final: 0.6499 (m-40) REVERT: F 49 LEU cc_start: 0.7418 (mp) cc_final: 0.6825 (mt) REVERT: F 59 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8386 (tttt) REVERT: F 85 ASP cc_start: 0.8698 (m-30) cc_final: 0.8143 (m-30) REVERT: G 35 ARG cc_start: 0.7430 (mtm180) cc_final: 0.7184 (ptp90) REVERT: H 37 TYR cc_start: 0.8047 (m-80) cc_final: 0.7600 (m-80) REVERT: H 42 TYR cc_start: 0.7126 (t80) cc_final: 0.6851 (t80) REVERT: H 45 LEU cc_start: 0.7677 (tp) cc_final: 0.7396 (tp) REVERT: H 57 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7833 (mmmt) REVERT: H 59 MET cc_start: 0.8299 (tpp) cc_final: 0.7803 (mmm) REVERT: H 61 ILE cc_start: 0.9130 (mt) cc_final: 0.8742 (mm) REVERT: H 65 PHE cc_start: 0.8710 (t80) cc_final: 0.8283 (t80) REVERT: H 68 ASP cc_start: 0.6642 (t0) cc_final: 0.5845 (t0) REVERT: H 71 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6800 (mt-10) REVERT: H 101 LEU cc_start: 0.8643 (mp) cc_final: 0.8391 (mt) REVERT: L 86 VAL cc_start: 0.4849 (t) cc_final: 0.4537 (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: 0.2142 (m-10) REVERT: N 41 VAL cc_start: 0.8862 (t) cc_final: 0.8631 (t) REVERT: N 54 ILE cc_start: 0.6872 (tt) cc_final: 0.6558 (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: 0.6658 (t0) REVERT: O 61 LEU cc_start: 0.8037 (mt) cc_final: 0.7536 (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: 0.7909 (tp40) REVERT: O 92 LEU cc_start: 0.8473 (mm) cc_final: 0.8145 (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: 0.8443 (tm-30) outliers start: 0 outliers final: 0 residues processed: 592 average time/residue: 0.1838 time to fit residues: 155.8378 Evaluate side-chains 376 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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: 40.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 50.0000 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 1.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.085951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063916 restraints weight = 126349.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065274 restraints weight = 70663.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.066199 restraints weight = 43286.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066368 restraints weight = 35188.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.066452 restraints weight = 31334.079| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 17 (22 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21551 Z= 0.239 Angle : 0.780 10.464 31255 Z= 0.447 Chirality : 0.048 0.368 3561 Planarity : 0.007 0.100 2220 Dihedral : 32.256 178.979 6852 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.67 % Allowed : 6.60 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.22), residues: 1219 helix: 1.38 (0.16), residues: 923 sheet: None (None), residues: 0 loop : -0.07 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.049 0.003 TYR B 88 PHE 0.028 0.003 PHE O 67 HIS 0.011 0.003 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.24 (21551) covalent geometry : angle 0.77991 / 0.45 (31255) hydrogen bonds : bond 0.07706 / 5.16 ( 1312) hydrogen bonds : angle 3.96294 / 2.90 ( 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 431 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 424 time to evaluate : 0.509 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: A 61 LEU cc_start: 0.8985 (mt) cc_final: 0.8662 (mp) REVERT: A 84 PHE cc_start: 0.8462 (m-80) cc_final: 0.8179 (m-10) REVERT: A 93 GLN cc_start: 0.9318 (tt0) cc_final: 0.8531 (tp40) REVERT: A 97 GLU cc_start: 0.8174 (pt0) cc_final: 0.7910 (pt0) REVERT: B 45 ARG cc_start: 0.7597 (tpt-90) cc_final: 0.6579 (tpp80) REVERT: B 68 ASP cc_start: 0.8843 (m-30) cc_final: 0.8589 (m-30) REVERT: B 88 TYR cc_start: 0.8547 (m-10) cc_final: 0.8243 (m-80) REVERT: B 98 TYR cc_start: 0.8504 (m-10) cc_final: 0.8215 (m-10) REVERT: C 39 TYR cc_start: 0.9100 (m-80) cc_final: 0.7895 (m-80) REVERT: C 110 ASN cc_start: 0.9165 (t0) cc_final: 0.8678 (m110) REVERT: D 34 LYS cc_start: 0.7441 (tptp) cc_final: 0.7031 (tppt) REVERT: D 44 VAL cc_start: 0.9349 (t) cc_final: 0.8975 (p) REVERT: D 68 ASP cc_start: 0.8544 (t70) cc_final: 0.8178 (t0) REVERT: D 82 HIS cc_start: 0.8375 (t-90) cc_final: 0.8061 (t70) REVERT: D 89 ILE cc_start: 0.8908 (mt) cc_final: 0.8402 (tt) REVERT: D 108 LYS cc_start: 0.9104 (mttm) cc_final: 0.8804 (mtpt) REVERT: E 46 VAL cc_start: 0.8176 (t) cc_final: 0.7723 (t) REVERT: E 50 GLU cc_start: 0.8094 (mp0) cc_final: 0.7860 (mm-30) REVERT: E 54 TYR cc_start: 0.8200 (m-10) cc_final: 0.6408 (m-80) REVERT: E 67 PHE cc_start: 0.7819 (t80) cc_final: 0.7526 (t80) REVERT: E 93 GLN cc_start: 0.9158 (tt0) cc_final: 0.7663 (tp-100) REVERT: F 44 LYS cc_start: 0.8609 (ttpp) cc_final: 0.7977 (mtpt) REVERT: F 59 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8024 (tttt) REVERT: F 60 VAL cc_start: 0.9238 (t) cc_final: 0.7639 (t) REVERT: F 79 LYS cc_start: 0.7043 (mmtt) cc_final: 0.6594 (tptp) REVERT: F 88 TYR cc_start: 0.8550 (m-80) cc_final: 0.8243 (m-80) REVERT: G 25 PHE cc_start: 0.8470 (m-80) cc_final: 0.7937 (m-80) REVERT: G 38 ASN cc_start: 0.7916 (m110) cc_final: 0.7548 (t0) REVERT: G 56 GLU cc_start: 0.8034 (tt0) cc_final: 0.7764 (pt0) REVERT: G 90 ASP cc_start: 0.8346 (t70) cc_final: 0.7987 (t0) REVERT: H 37 TYR cc_start: 0.8916 (m-80) cc_final: 0.8617 (m-80) REVERT: H 61 ILE cc_start: 0.8914 (mt) cc_final: 0.8681 (mm) REVERT: H 65 PHE cc_start: 0.9095 (t80) cc_final: 0.8564 (t80) REVERT: H 68 ASP cc_start: 0.8322 (t0) cc_final: 0.7430 (t0) REVERT: K 107 THR cc_start: 0.9216 (p) cc_final: 0.9002 (p) REVERT: M 64 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8217 (tm-30) REVERT: M 84 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8578 (tm-30) REVERT: N 68 ASP cc_start: 0.8624 (t70) cc_final: 0.8288 (t0) REVERT: N 71 GLU cc_start: 0.8821 (pp20) cc_final: 0.8365 (pp20) REVERT: O 60 LEU cc_start: 0.5504 (mp) cc_final: 0.4070 (mp) REVERT: O 61 LEU cc_start: 0.8696 (mt) cc_final: 0.7869 (mp) REVERT: O 76 GLN cc_start: 0.9229 (tt0) cc_final: 0.8781 (tp40) REVERT: O 96 CYS cc_start: 0.9442 (m) cc_final: 0.9152 (m) REVERT: O 120 MET cc_start: 0.8116 (ttp) cc_final: 0.7904 (ttm) REVERT: O 123 ASP cc_start: 0.9414 (m-30) cc_final: 0.9179 (m-30) REVERT: P 57 VAL cc_start: 0.9298 (t) cc_final: 0.9097 (p) REVERT: P 84 MET cc_start: 0.6991 (tpp) cc_final: 0.6576 (tpp) REVERT: P 93 GLN cc_start: 0.8634 (tt0) cc_final: 0.8360 (tm-30) outliers start: 7 outliers final: 3 residues processed: 427 average time/residue: 0.1414 time to fit residues: 93.1505 Evaluate side-chains 321 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 318 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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: 6.9990 chunk 23 optimal weight: 2.9990 chunk 107 optimal weight: 40.0000 chunk 94 optimal weight: 50.0000 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 chunk 155 optimal weight: 6.9990 chunk 97 optimal weight: 50.0000 chunk 121 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 93 GLN G 31 HIS ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.077343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.055496 restraints weight = 120899.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.056860 restraints weight = 62315.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.057759 restraints weight = 40605.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.058271 restraints weight = 31232.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.058673 restraints weight = 26917.597| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21551 Z= 0.236 Angle : 0.763 11.324 31255 Z= 0.436 Chirality : 0.048 0.362 3561 Planarity : 0.006 0.063 2220 Dihedral : 32.661 179.705 6852 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.57 % Allowed : 5.64 % Favored : 93.79 % 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: 1.35 (0.22), residues: 1219 helix: 1.27 (0.16), residues: 923 sheet: None (None), residues: 0 loop : -0.09 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 92 TYR 0.035 0.003 TYR B 88 PHE 0.021 0.003 PHE D 65 HIS 0.009 0.002 HIS M 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.24 (21551) covalent geometry : angle 0.76302 / 0.44 (31255) hydrogen bonds : bond 0.07071 / 4.67 ( 1312) hydrogen bonds : angle 3.92528 / 2.87 ( 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 400 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 394 time to evaluate : 0.543 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: 0.8874 (tp40) cc_final: 0.8628 (tp40) REVERT: A 82 LEU cc_start: 0.7880 (mt) cc_final: 0.7658 (mt) REVERT: A 84 PHE cc_start: 0.8396 (m-80) cc_final: 0.8157 (m-10) REVERT: A 93 GLN cc_start: 0.9331 (tt0) cc_final: 0.8534 (tp40) REVERT: A 110 CYS cc_start: 0.9416 (m) cc_final: 0.9190 (m) REVERT: B 45 ARG cc_start: 0.7708 (tpt-90) cc_final: 0.6429 (tpp80) REVERT: B 67 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7893 (tpp80) REVERT: B 74 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 88 TYR cc_start: 0.8412 (m-10) cc_final: 0.8045 (m-10) REVERT: C 56 GLU cc_start: 0.8896 (tt0) cc_final: 0.8402 (tt0) REVERT: C 110 ASN cc_start: 0.9110 (t0) cc_final: 0.8747 (m110) REVERT: D 44 VAL cc_start: 0.9435 (t) cc_final: 0.9074 (p) REVERT: D 82 HIS cc_start: 0.8552 (t-90) cc_final: 0.8243 (t70) REVERT: D 108 LYS cc_start: 0.9097 (mttm) cc_final: 0.8809 (mtpt) REVERT: E 46 VAL cc_start: 0.7898 (t) cc_final: 0.7484 (t) REVERT: E 81 ASP cc_start: 0.7765 (t0) cc_final: 0.7482 (t0) REVERT: F 59 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8172 (tttt) REVERT: F 60 VAL cc_start: 0.9224 (t) cc_final: 0.8853 (t) REVERT: F 79 LYS cc_start: 0.7348 (mmtt) cc_final: 0.6840 (tptp) REVERT: F 88 TYR cc_start: 0.8661 (m-10) cc_final: 0.8439 (m-80) REVERT: F 93 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8887 (tm-30) REVERT: G 35 ARG cc_start: 0.8868 (ptp-110) cc_final: 0.8304 (ptp90) REVERT: H 54 ILE cc_start: 0.8731 (mp) cc_final: 0.8530 (mp) REVERT: H 68 ASP cc_start: 0.8701 (t0) cc_final: 0.7953 (t0) REVERT: H 87 SER cc_start: 0.8177 (m) cc_final: 0.7874 (p) REVERT: H 93 GLU cc_start: 0.9276 (mp0) cc_final: 0.9053 (mp0) REVERT: H 94 ILE cc_start: 0.9507 (mm) cc_final: 0.9299 (mm) REVERT: H 112 SER cc_start: 0.9445 (t) cc_final: 0.9022 (p) REVERT: K 107 THR cc_start: 0.9374 (p) cc_final: 0.9147 (p) REVERT: L 30 THR cc_start: 0.7272 (p) cc_final: 0.6988 (p) REVERT: L 62 LEU cc_start: 0.9718 (mm) cc_final: 0.9480 (mm) REVERT: M 25 PHE cc_start: 0.7676 (m-10) cc_final: 0.7200 (m-10) REVERT: M 58 LEU cc_start: 0.9035 (mp) cc_final: 0.8761 (pp) REVERT: M 64 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8388 (tm-30) REVERT: M 76 THR cc_start: 0.8615 (m) cc_final: 0.8361 (p) REVERT: M 84 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8575 (tm-30) REVERT: N 68 ASP cc_start: 0.8674 (t70) cc_final: 0.8374 (t0) REVERT: N 71 GLU cc_start: 0.8788 (pp20) cc_final: 0.8400 (pp20) REVERT: O 61 LEU cc_start: 0.8641 (mt) cc_final: 0.7411 (mp) REVERT: O 65 LEU cc_start: 0.8205 (tp) cc_final: 0.7938 (tp) REVERT: O 76 GLN cc_start: 0.9289 (tt0) cc_final: 0.8812 (tp40) REVERT: O 90 MET cc_start: 0.9199 (ptp) cc_final: 0.8908 (ptp) REVERT: O 96 CYS cc_start: 0.9447 (m) cc_final: 0.9041 (m) REVERT: P 93 GLN cc_start: 0.8493 (tt0) cc_final: 0.8093 (tm-30) outliers start: 6 outliers final: 2 residues processed: 395 average time/residue: 0.1444 time to fit residues: 88.5275 Evaluate side-chains 300 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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: 5.9990 chunk 87 optimal weight: 50.0000 chunk 78 optimal weight: 50.0000 chunk 123 optimal weight: 10.0000 chunk 161 optimal weight: 0.6980 chunk 110 optimal weight: 50.0000 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 75 optimal weight: 40.0000 chunk 115 optimal weight: 40.0000 chunk 32 optimal weight: 0.6980 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** M 68 ASN O 125 GLN P 64 ASN P 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.078427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.055836 restraints weight = 119874.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.057314 restraints weight = 60234.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.058266 restraints weight = 38871.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.058841 restraints weight = 29699.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.059236 restraints weight = 25375.749| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21551 Z= 0.166 Angle : 0.697 8.649 31255 Z= 0.402 Chirality : 0.046 0.368 3561 Planarity : 0.005 0.050 2220 Dihedral : 32.718 179.945 6852 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.10 % Allowed : 2.49 % Favored : 97.42 % 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: 1.55 (0.23), residues: 1219 helix: 1.43 (0.16), residues: 927 sheet: None (None), residues: 0 loop : -0.08 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 92 TYR 0.028 0.002 TYR P 88 PHE 0.018 0.002 PHE A 67 HIS 0.007 0.001 HIS M 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.17 (21551) covalent geometry : angle 0.69665 / 0.40 (31255) hydrogen bonds : bond 0.05784 / 3.84 ( 1312) hydrogen bonds : angle 3.65760 / 2.68 ( 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 395 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 0.509 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: A 62 ILE cc_start: 0.9125 (mt) cc_final: 0.8391 (mt) REVERT: A 84 PHE cc_start: 0.8331 (m-80) cc_final: 0.7997 (m-80) REVERT: A 93 GLN cc_start: 0.9280 (tt0) cc_final: 0.8567 (tp40) REVERT: A 110 CYS cc_start: 0.9348 (m) cc_final: 0.9139 (m) REVERT: B 63 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 67 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7830 (tpp80) REVERT: B 68 ASP cc_start: 0.9097 (m-30) cc_final: 0.8869 (m-30) REVERT: B 74 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 88 TYR cc_start: 0.8326 (m-10) cc_final: 0.6942 (m-10) REVERT: C 35 ARG cc_start: 0.8994 (mtt90) cc_final: 0.8596 (mmt180) REVERT: C 56 GLU cc_start: 0.8901 (tt0) cc_final: 0.8357 (tt0) REVERT: C 104 GLN cc_start: 0.8454 (mt0) cc_final: 0.8096 (mt0) REVERT: C 110 ASN cc_start: 0.9055 (t0) cc_final: 0.8633 (m110) REVERT: D 44 VAL cc_start: 0.9407 (t) cc_final: 0.9033 (p) REVERT: D 82 HIS cc_start: 0.8405 (t-90) cc_final: 0.8143 (t70) REVERT: D 89 ILE cc_start: 0.8732 (mt) cc_final: 0.8311 (tt) REVERT: D 100 LEU cc_start: 0.9162 (mm) cc_final: 0.8904 (mm) REVERT: D 108 LYS cc_start: 0.9156 (mttm) cc_final: 0.8933 (mtpt) REVERT: E 54 TYR cc_start: 0.7961 (m-10) cc_final: 0.7278 (m-80) REVERT: E 57 SER cc_start: 0.8895 (t) cc_final: 0.8332 (p) REVERT: E 59 GLU cc_start: 0.8239 (pm20) cc_final: 0.7930 (pm20) REVERT: E 90 MET cc_start: 0.9075 (mmm) cc_final: 0.8797 (tmm) REVERT: E 105 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8527 (tm-30) REVERT: E 109 LEU cc_start: 0.9161 (mp) cc_final: 0.8901 (mt) REVERT: F 59 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7956 (tttt) REVERT: F 60 VAL cc_start: 0.9388 (t) cc_final: 0.8464 (t) REVERT: F 93 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8918 (tm-30) REVERT: G 35 ARG cc_start: 0.8793 (ptp-110) cc_final: 0.8122 (ptp90) REVERT: G 95 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7833 (tmtt) REVERT: H 37 TYR cc_start: 0.8797 (m-80) cc_final: 0.7892 (m-80) REVERT: H 61 ILE cc_start: 0.8715 (mm) cc_final: 0.8304 (mt) REVERT: H 68 ASP cc_start: 0.8731 (t0) cc_final: 0.7914 (t0) REVERT: H 93 GLU cc_start: 0.9251 (mp0) cc_final: 0.9030 (mp0) REVERT: H 94 ILE cc_start: 0.9484 (mm) cc_final: 0.9271 (mm) REVERT: H 106 LEU cc_start: 0.9483 (mt) cc_final: 0.8996 (mt) REVERT: H 112 SER cc_start: 0.9193 (t) cc_final: 0.8939 (p) REVERT: K 90 MET cc_start: 0.8800 (mmp) cc_final: 0.8479 (mmp) REVERT: K 107 THR cc_start: 0.9332 (p) cc_final: 0.9109 (p) REVERT: L 62 LEU cc_start: 0.9704 (mm) cc_final: 0.9467 (mm) REVERT: L 85 ASP cc_start: 0.5201 (m-30) cc_final: 0.4591 (m-30) REVERT: M 64 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8373 (tm-30) REVERT: M 84 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8523 (tm-30) REVERT: M 107 VAL cc_start: 0.8833 (t) cc_final: 0.8596 (p) REVERT: N 68 ASP cc_start: 0.8665 (t70) cc_final: 0.8368 (t0) REVERT: N 71 GLU cc_start: 0.8701 (pp20) cc_final: 0.8202 (pp20) REVERT: O 64 LYS cc_start: 0.8448 (pptt) cc_final: 0.8214 (pptt) REVERT: O 65 LEU cc_start: 0.8102 (tp) cc_final: 0.7719 (tp) REVERT: O 68 GLN cc_start: 0.9075 (mt0) cc_final: 0.8833 (mt0) REVERT: O 76 GLN cc_start: 0.9288 (tt0) cc_final: 0.8791 (tp40) REVERT: O 96 CYS cc_start: 0.9359 (m) cc_final: 0.8994 (m) REVERT: O 120 MET cc_start: 0.8752 (ttt) cc_final: 0.8484 (ttp) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.1339 time to fit residues: 82.7612 Evaluate side-chains 313 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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: 0.6980 chunk 163 optimal weight: 6.9990 chunk 74 optimal weight: 40.0000 chunk 17 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 113 optimal weight: 50.0000 chunk 105 optimal weight: 50.0000 chunk 82 optimal weight: 30.0000 chunk 137 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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** D 95 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN M 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.076334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.053851 restraints weight = 121458.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.055276 restraints weight = 61251.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056193 restraints weight = 39450.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056796 restraints weight = 30051.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057104 restraints weight = 25656.527| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21551 Z= 0.211 Angle : 0.734 9.200 31255 Z= 0.418 Chirality : 0.047 0.358 3561 Planarity : 0.006 0.054 2220 Dihedral : 32.839 179.804 6852 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.10 % Allowed : 3.73 % Favored : 96.18 % 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: 1.32 (0.22), residues: 1219 helix: 1.31 (0.16), residues: 926 sheet: None (None), residues: 0 loop : -0.34 (0.32), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 92 TYR 0.039 0.003 TYR L 88 PHE 0.017 0.002 PHE A 67 HIS 0.006 0.002 HIS M 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 (21551) covalent geometry : angle 0.73363 / 0.42 (31255) hydrogen bonds : bond 0.06927 / 4.62 ( 1312) hydrogen bonds : angle 3.80587 / 2.76 ( 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 371 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 0.341 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: A 62 ILE cc_start: 0.9183 (mt) cc_final: 0.8481 (mt) REVERT: A 84 PHE cc_start: 0.8441 (m-80) cc_final: 0.8139 (m-10) REVERT: A 93 GLN cc_start: 0.9306 (tt0) cc_final: 0.8591 (tp40) REVERT: A 110 CYS cc_start: 0.9312 (m) cc_final: 0.9104 (m) REVERT: B 63 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8211 (tm-30) REVERT: B 64 ASN cc_start: 0.9350 (t0) cc_final: 0.9075 (t0) REVERT: B 67 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7411 (ttm110) REVERT: B 68 ASP cc_start: 0.9076 (m-30) cc_final: 0.8746 (m-30) REVERT: B 74 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7889 (tm-30) REVERT: B 88 TYR cc_start: 0.8038 (m-10) cc_final: 0.7695 (m-80) REVERT: C 35 ARG cc_start: 0.9068 (mtt90) cc_final: 0.8572 (mmt-90) REVERT: C 56 GLU cc_start: 0.8884 (tt0) cc_final: 0.8470 (tt0) REVERT: C 110 ASN cc_start: 0.8964 (t0) cc_final: 0.8619 (m110) REVERT: C 111 ILE cc_start: 0.8971 (mp) cc_final: 0.8769 (mp) REVERT: D 44 VAL cc_start: 0.9462 (t) cc_final: 0.9127 (p) REVERT: D 82 HIS cc_start: 0.8393 (t-90) cc_final: 0.8004 (t70) REVERT: D 89 ILE cc_start: 0.8776 (mt) cc_final: 0.8374 (tt) REVERT: D 100 LEU cc_start: 0.9174 (mm) cc_final: 0.8901 (mm) REVERT: E 54 TYR cc_start: 0.8025 (m-10) cc_final: 0.7351 (m-80) REVERT: E 57 SER cc_start: 0.8830 (t) cc_final: 0.8361 (p) REVERT: E 59 GLU cc_start: 0.8376 (pm20) cc_final: 0.8053 (pm20) REVERT: E 93 GLN cc_start: 0.8761 (tt0) cc_final: 0.7753 (tm-30) REVERT: E 94 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8466 (mt-10) REVERT: E 97 GLU cc_start: 0.8088 (pm20) cc_final: 0.7869 (pm20) REVERT: E 105 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8191 (tm-30) REVERT: E 106 ASP cc_start: 0.9316 (m-30) cc_final: 0.9057 (m-30) REVERT: E 110 CYS cc_start: 0.9164 (m) cc_final: 0.8896 (m) REVERT: F 59 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8178 (tttt) REVERT: F 60 VAL cc_start: 0.9173 (t) cc_final: 0.8747 (t) REVERT: F 93 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8741 (tm-30) REVERT: G 35 ARG cc_start: 0.8803 (ptp-110) cc_final: 0.8175 (ptp90) REVERT: H 59 MET cc_start: 0.9029 (tpp) cc_final: 0.8658 (tpp) REVERT: H 68 ASP cc_start: 0.8635 (t0) cc_final: 0.7864 (t0) REVERT: H 94 ILE cc_start: 0.9481 (mm) cc_final: 0.9221 (mm) REVERT: H 112 SER cc_start: 0.9220 (t) cc_final: 0.8921 (p) REVERT: K 103 LEU cc_start: 0.9370 (mt) cc_final: 0.9059 (mt) REVERT: L 88 TYR cc_start: 0.5308 (m-80) cc_final: 0.4743 (m-10) REVERT: M 57 TYR cc_start: 0.8932 (t80) cc_final: 0.8423 (t80) REVERT: M 61 GLU cc_start: 0.9335 (pt0) cc_final: 0.9109 (pt0) REVERT: M 64 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8276 (tm-30) REVERT: M 84 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8581 (tm-30) REVERT: N 68 ASP cc_start: 0.8919 (t0) cc_final: 0.8374 (t0) REVERT: N 71 GLU cc_start: 0.8665 (pp20) cc_final: 0.8300 (pp20) REVERT: N 76 GLU cc_start: 0.7071 (tp30) cc_final: 0.6749 (tp30) REVERT: O 51 ILE cc_start: 0.9374 (mm) cc_final: 0.8995 (mm) REVERT: O 54 TYR cc_start: 0.9146 (m-80) cc_final: 0.8545 (m-80) REVERT: O 76 GLN cc_start: 0.9112 (tt0) cc_final: 0.8631 (tp40) REVERT: O 96 CYS cc_start: 0.9518 (m) cc_final: 0.9148 (m) REVERT: O 101 VAL cc_start: 0.9285 (m) cc_final: 0.8796 (p) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 0.1279 time to fit residues: 74.4140 Evaluate side-chains 294 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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: 50.0000 chunk 156 optimal weight: 8.9990 chunk 73 optimal weight: 40.0000 chunk 93 optimal weight: 50.0000 chunk 120 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 166 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 84 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 = 0.3761 r_free = 0.3761 target = 0.075460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053683 restraints weight = 117047.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.055153 restraints weight = 57876.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056101 restraints weight = 36403.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056695 restraints weight = 27206.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057025 restraints weight = 22842.747| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21551 Z= 0.195 Angle : 0.724 9.218 31255 Z= 0.413 Chirality : 0.047 0.358 3561 Planarity : 0.006 0.058 2220 Dihedral : 32.944 179.169 6852 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.22), residues: 1219 helix: 1.26 (0.16), residues: 928 sheet: None (None), residues: 0 loop : -0.44 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG O 53 TYR 0.033 0.003 TYR F 88 PHE 0.019 0.003 PHE N 65 HIS 0.009 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.20 (21551) covalent geometry : angle 0.72358 / 0.41 (31255) hydrogen bonds : bond 0.06144 / 4.09 ( 1312) hydrogen bonds : angle 3.79086 / 2.78 ( 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 372 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.513 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 62 ILE cc_start: 0.9218 (mt) cc_final: 0.8546 (mt) REVERT: A 84 PHE cc_start: 0.8476 (m-80) cc_final: 0.8156 (m-80) REVERT: A 93 GLN cc_start: 0.9284 (tt0) cc_final: 0.8596 (tp40) REVERT: A 120 MET cc_start: 0.9131 (mtm) cc_final: 0.8855 (mtp) REVERT: B 63 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8383 (tm-30) REVERT: B 64 ASN cc_start: 0.9310 (t0) cc_final: 0.9031 (t0) REVERT: B 68 ASP cc_start: 0.9082 (m-30) cc_final: 0.8851 (m-30) REVERT: B 74 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 88 TYR cc_start: 0.7763 (m-10) cc_final: 0.7322 (m-10) REVERT: C 56 GLU cc_start: 0.8910 (tt0) cc_final: 0.7918 (tt0) REVERT: C 110 ASN cc_start: 0.8956 (t0) cc_final: 0.8662 (m110) REVERT: D 44 VAL cc_start: 0.9446 (t) cc_final: 0.9103 (p) REVERT: D 83 TYR cc_start: 0.8425 (t80) cc_final: 0.7914 (t80) REVERT: D 89 ILE cc_start: 0.8808 (mt) cc_final: 0.8419 (tt) REVERT: D 96 THR cc_start: 0.9459 (t) cc_final: 0.9186 (p) REVERT: D 100 LEU cc_start: 0.9163 (mm) cc_final: 0.8926 (mm) REVERT: D 108 LYS cc_start: 0.9184 (mttm) cc_final: 0.8933 (mtpt) REVERT: E 54 TYR cc_start: 0.8004 (m-10) cc_final: 0.7377 (m-80) REVERT: E 57 SER cc_start: 0.8862 (t) cc_final: 0.8535 (p) REVERT: E 59 GLU cc_start: 0.8215 (pm20) cc_final: 0.7913 (pm20) REVERT: E 82 LEU cc_start: 0.7764 (pt) cc_final: 0.7553 (pt) REVERT: E 93 GLN cc_start: 0.8886 (tt0) cc_final: 0.7677 (tp40) REVERT: E 94 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8486 (mt-10) REVERT: E 106 ASP cc_start: 0.9263 (m-30) cc_final: 0.9040 (m-30) REVERT: F 44 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8449 (mtpp) REVERT: F 59 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7923 (tttt) REVERT: F 79 LYS cc_start: 0.7284 (mmtt) cc_final: 0.6647 (mmtt) REVERT: F 93 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8802 (tm-30) REVERT: G 35 ARG cc_start: 0.8849 (ptp-110) cc_final: 0.8363 (ptp90) REVERT: G 38 ASN cc_start: 0.8758 (m110) cc_final: 0.8440 (m110) REVERT: G 68 ASN cc_start: 0.9242 (m110) cc_final: 0.8876 (m-40) REVERT: H 37 TYR cc_start: 0.8863 (m-80) cc_final: 0.7987 (m-10) REVERT: H 59 MET cc_start: 0.9049 (tpp) cc_final: 0.8622 (tpp) REVERT: H 68 ASP cc_start: 0.8629 (t0) cc_final: 0.7895 (t0) REVERT: H 112 SER cc_start: 0.9128 (t) cc_final: 0.8821 (p) REVERT: H 113 GLU cc_start: 0.8535 (mp0) cc_final: 0.8081 (mp0) REVERT: K 103 LEU cc_start: 0.9302 (mt) cc_final: 0.9014 (mt) REVERT: M 57 TYR cc_start: 0.8969 (t80) cc_final: 0.8542 (t80) REVERT: M 61 GLU cc_start: 0.9280 (pt0) cc_final: 0.8861 (pt0) REVERT: M 64 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8211 (tm-30) REVERT: M 79 ILE cc_start: 0.8174 (tp) cc_final: 0.7890 (mt) REVERT: M 84 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8572 (tm-30) REVERT: O 76 GLN cc_start: 0.9086 (tt0) cc_final: 0.8579 (tp40) REVERT: O 96 CYS cc_start: 0.9460 (m) cc_final: 0.9041 (m) REVERT: O 101 VAL cc_start: 0.9462 (m) cc_final: 0.9001 (p) REVERT: O 105 GLU cc_start: 0.9283 (pt0) cc_final: 0.9072 (pt0) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.1376 time to fit residues: 80.9177 Evaluate side-chains 289 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 0.6980 chunk 75 optimal weight: 40.0000 chunk 131 optimal weight: 3.9990 chunk 133 optimal weight: 30.0000 chunk 83 optimal weight: 40.0000 chunk 121 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 113 optimal weight: 50.0000 chunk 91 optimal weight: 50.0000 chunk 58 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 95 GLN G 31 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.075666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054023 restraints weight = 117404.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.055506 restraints weight = 57783.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.056445 restraints weight = 36393.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057042 restraints weight = 27181.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057369 restraints weight = 22893.503| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21551 Z= 0.178 Angle : 0.718 8.454 31255 Z= 0.409 Chirality : 0.047 0.357 3561 Planarity : 0.006 0.051 2220 Dihedral : 32.960 177.602 6852 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.10 % Allowed : 1.72 % Favored : 98.18 % 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: 1.20 (0.23), residues: 1219 helix: 1.25 (0.16), residues: 927 sheet: None (None), residues: 0 loop : -0.48 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 92 TYR 0.053 0.003 TYR F 88 PHE 0.022 0.002 PHE N 65 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.18 (21551) covalent geometry : angle 0.71794 / 0.41 (31255) hydrogen bonds : bond 0.05899 / 3.92 ( 1312) hydrogen bonds : angle 3.75109 / 2.75 ( 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 : 0.517 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: A 62 ILE cc_start: 0.9235 (mt) cc_final: 0.8554 (mt) REVERT: A 84 PHE cc_start: 0.8417 (m-80) cc_final: 0.8065 (m-80) REVERT: A 93 GLN cc_start: 0.9262 (tt0) cc_final: 0.8573 (tp40) REVERT: A 110 CYS cc_start: 0.9309 (m) cc_final: 0.9088 (m) REVERT: A 120 MET cc_start: 0.9097 (mtm) cc_final: 0.8788 (mtp) REVERT: B 45 ARG cc_start: 0.8320 (tpt-90) cc_final: 0.6578 (tpt-90) REVERT: B 63 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 67 ARG cc_start: 0.8720 (tpp80) cc_final: 0.8243 (tpp80) REVERT: B 68 ASP cc_start: 0.9104 (m-30) cc_final: 0.8811 (m-30) REVERT: B 74 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 56 GLU cc_start: 0.8922 (tt0) cc_final: 0.7952 (tt0) REVERT: C 104 GLN cc_start: 0.8235 (mt0) cc_final: 0.7949 (mm-40) REVERT: C 110 ASN cc_start: 0.8942 (t0) cc_final: 0.8716 (m110) REVERT: C 111 ILE cc_start: 0.8960 (mp) cc_final: 0.8506 (mt) REVERT: D 42 TYR cc_start: 0.8565 (t80) cc_final: 0.8356 (t80) REVERT: D 44 VAL cc_start: 0.9445 (t) cc_final: 0.9098 (p) REVERT: D 89 ILE cc_start: 0.8817 (mt) cc_final: 0.8430 (tt) REVERT: D 96 THR cc_start: 0.9375 (t) cc_final: 0.9129 (p) REVERT: D 100 LEU cc_start: 0.9114 (mm) cc_final: 0.8886 (mm) REVERT: E 54 TYR cc_start: 0.8013 (m-10) cc_final: 0.7356 (m-80) REVERT: E 57 SER cc_start: 0.8904 (t) cc_final: 0.8573 (p) REVERT: F 44 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8352 (mtpp) REVERT: F 60 VAL cc_start: 0.9190 (t) cc_final: 0.8723 (t) REVERT: F 79 LYS cc_start: 0.7421 (mmtt) cc_final: 0.6761 (mmtt) REVERT: F 84 MET cc_start: 0.8251 (tpp) cc_final: 0.7995 (tpp) REVERT: F 88 TYR cc_start: 0.8521 (m-80) cc_final: 0.7761 (m-80) REVERT: F 93 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8804 (tm-30) REVERT: G 68 ASN cc_start: 0.9192 (m110) cc_final: 0.8891 (m-40) REVERT: H 37 TYR cc_start: 0.8816 (m-80) cc_final: 0.7956 (m-10) REVERT: H 59 MET cc_start: 0.9040 (tpp) cc_final: 0.8642 (tpp) REVERT: H 68 ASP cc_start: 0.8681 (t0) cc_final: 0.7968 (t0) REVERT: H 94 ILE cc_start: 0.9179 (mm) cc_final: 0.8975 (mm) REVERT: H 112 SER cc_start: 0.9125 (t) cc_final: 0.8668 (p) REVERT: K 103 LEU cc_start: 0.9292 (mt) cc_final: 0.9004 (mt) REVERT: L 88 TYR cc_start: 0.5243 (m-80) cc_final: 0.4877 (m-10) REVERT: M 57 TYR cc_start: 0.8860 (t80) cc_final: 0.8459 (t80) REVERT: M 61 GLU cc_start: 0.9193 (pt0) cc_final: 0.8755 (pt0) REVERT: M 64 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8309 (tm-30) REVERT: M 79 ILE cc_start: 0.8333 (tp) cc_final: 0.8084 (mt) REVERT: N 76 GLU cc_start: 0.6826 (tp30) cc_final: 0.6554 (tp30) REVERT: N 102 LEU cc_start: 0.8041 (mp) cc_final: 0.7779 (mt) REVERT: O 76 GLN cc_start: 0.9079 (tt0) cc_final: 0.8537 (tp40) REVERT: O 96 CYS cc_start: 0.9592 (m) cc_final: 0.9200 (m) REVERT: O 101 VAL cc_start: 0.9458 (m) cc_final: 0.8956 (p) REVERT: O 105 GLU cc_start: 0.9214 (pt0) cc_final: 0.8979 (pt0) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.1406 time to fit residues: 79.6482 Evaluate side-chains 290 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 0.6980 chunk 53 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 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: 30.0000 chunk 25 optimal weight: 9.9990 chunk 71 optimal weight: 50.0000 chunk 26 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** 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 108 ASN M 68 ASN P 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.075681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053721 restraints weight = 117925.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.055225 restraints weight = 57691.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.056191 restraints weight = 36298.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.056781 restraints weight = 27146.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.057171 restraints weight = 22900.913| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4899 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= 0.176 Angle : 0.719 7.892 31255 Z= 0.411 Chirality : 0.047 0.356 3561 Planarity : 0.006 0.056 2220 Dihedral : 32.967 178.608 6852 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.10 % Allowed : 1.05 % 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: 0.99 (0.22), residues: 1219 helix: 1.12 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -0.71 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 42 TYR 0.042 0.003 TYR B 88 PHE 0.015 0.002 PHE B 61 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (21551) covalent geometry : angle 0.71937 / 0.41 (31255) hydrogen bonds : bond 0.05816 / 3.87 ( 1312) hydrogen bonds : angle 3.80820 / 2.77 ( 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 363 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 362 time to evaluate : 0.453 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: A 62 ILE cc_start: 0.9227 (mt) cc_final: 0.8554 (mt) REVERT: A 84 PHE cc_start: 0.8370 (m-80) cc_final: 0.7970 (m-80) REVERT: A 93 GLN cc_start: 0.9277 (tt0) cc_final: 0.8820 (tp40) REVERT: A 120 MET cc_start: 0.9160 (mtm) cc_final: 0.8936 (mtp) REVERT: B 63 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 74 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 85 ASP cc_start: 0.8839 (m-30) cc_final: 0.8357 (m-30) REVERT: B 88 TYR cc_start: 0.7483 (m-10) cc_final: 0.7262 (m-10) REVERT: B 98 TYR cc_start: 0.8566 (m-10) cc_final: 0.8261 (m-80) REVERT: C 56 GLU cc_start: 0.8934 (tt0) cc_final: 0.8209 (tt0) REVERT: D 42 TYR cc_start: 0.8611 (t80) cc_final: 0.8402 (t80) REVERT: D 44 VAL cc_start: 0.9450 (t) cc_final: 0.9090 (p) REVERT: D 89 ILE cc_start: 0.8634 (mt) cc_final: 0.8223 (tt) REVERT: D 96 THR cc_start: 0.9380 (t) cc_final: 0.9083 (p) REVERT: D 100 LEU cc_start: 0.9198 (mm) cc_final: 0.8949 (mm) REVERT: E 54 TYR cc_start: 0.8001 (m-10) cc_final: 0.7260 (m-80) REVERT: E 57 SER cc_start: 0.8997 (t) cc_final: 0.8605 (p) REVERT: E 59 GLU cc_start: 0.8179 (pm20) cc_final: 0.7735 (pm20) REVERT: E 67 PHE cc_start: 0.8200 (t80) cc_final: 0.7965 (t80) REVERT: E 82 LEU cc_start: 0.7792 (pt) cc_final: 0.7559 (pt) REVERT: F 39 ARG cc_start: 0.8906 (mmt90) cc_final: 0.8694 (mmm-85) REVERT: F 44 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8364 (mtpp) REVERT: F 60 VAL cc_start: 0.9179 (t) cc_final: 0.8786 (t) REVERT: F 79 LYS cc_start: 0.7412 (mmtt) cc_final: 0.6727 (mmtt) REVERT: F 85 ASP cc_start: 0.8352 (m-30) cc_final: 0.8049 (m-30) REVERT: F 88 TYR cc_start: 0.8358 (m-80) cc_final: 0.7577 (m-80) REVERT: F 93 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8659 (tm-30) REVERT: G 38 ASN cc_start: 0.8633 (m110) cc_final: 0.8421 (m110) REVERT: G 68 ASN cc_start: 0.9197 (m110) cc_final: 0.8877 (m-40) REVERT: G 95 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7991 (tmtt) REVERT: H 37 TYR cc_start: 0.8824 (m-80) cc_final: 0.7924 (m-10) REVERT: H 59 MET cc_start: 0.9044 (tpp) cc_final: 0.8583 (tpp) REVERT: H 68 ASP cc_start: 0.8725 (t0) cc_final: 0.7947 (t0) REVERT: H 113 GLU cc_start: 0.8589 (mp0) cc_final: 0.8017 (mp0) REVERT: K 103 LEU cc_start: 0.9290 (mt) cc_final: 0.9005 (mt) REVERT: K 107 THR cc_start: 0.9223 (p) cc_final: 0.8361 (p) REVERT: K 123 ASP cc_start: 0.8467 (m-30) cc_final: 0.7303 (t0) REVERT: L 88 TYR cc_start: 0.5894 (m-80) cc_final: 0.5559 (m-10) REVERT: M 64 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8350 (tm-30) REVERT: M 84 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8472 (tm-30) REVERT: N 102 LEU cc_start: 0.7975 (mp) cc_final: 0.7706 (mt) REVERT: O 54 TYR cc_start: 0.8554 (m-80) cc_final: 0.8337 (m-80) REVERT: O 76 GLN cc_start: 0.9080 (tt0) cc_final: 0.8531 (tp40) REVERT: O 96 CYS cc_start: 0.9575 (m) cc_final: 0.9181 (m) REVERT: O 101 VAL cc_start: 0.9467 (m) cc_final: 0.8986 (p) REVERT: O 105 GLU cc_start: 0.9253 (pt0) cc_final: 0.8972 (pt0) outliers start: 1 outliers final: 0 residues processed: 363 average time/residue: 0.1228 time to fit residues: 70.9614 Evaluate side-chains 289 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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: 3.9990 chunk 97 optimal weight: 50.0000 chunk 163 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 40.0000 chunk 103 optimal weight: 50.0000 chunk 83 optimal weight: 40.0000 chunk 109 optimal weight: 20.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN M 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.072112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.050406 restraints weight = 120567.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051817 restraints weight = 59267.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.052705 restraints weight = 37617.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053264 restraints weight = 28429.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.053568 restraints weight = 24152.541| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 21551 Z= 0.323 Angle : 0.863 11.550 31255 Z= 0.482 Chirality : 0.053 0.342 3561 Planarity : 0.008 0.083 2220 Dihedral : 33.331 175.804 6852 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 0.03 (0.22), residues: 1219 helix: 0.38 (0.15), residues: 929 sheet: None (None), residues: 0 loop : -0.83 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 92 TYR 0.057 0.004 TYR F 88 PHE 0.028 0.004 PHE D 65 HIS 0.015 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.32 (21551) covalent geometry : angle 0.86337 / 0.48 (31255) hydrogen bonds : bond 0.10061 / 6.71 ( 1312) hydrogen bonds : angle 4.42424 / 3.25 ( 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 342 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.500 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: 0.8558 (m-80) cc_final: 0.8232 (m-10) REVERT: A 105 GLU cc_start: 0.7357 (pp20) cc_final: 0.7117 (pp20) REVERT: A 110 CYS cc_start: 0.9344 (m) cc_final: 0.9065 (m) REVERT: A 120 MET cc_start: 0.9097 (mtm) cc_final: 0.8795 (mtp) REVERT: B 44 LYS cc_start: 0.8090 (tttm) cc_final: 0.7400 (tttt) REVERT: B 52 GLU cc_start: 0.8375 (mp0) cc_final: 0.8091 (mp0) REVERT: B 74 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 85 ASP cc_start: 0.8551 (m-30) cc_final: 0.8067 (m-30) REVERT: B 98 TYR cc_start: 0.8817 (m-10) cc_final: 0.8254 (m-10) REVERT: C 56 GLU cc_start: 0.8655 (tt0) cc_final: 0.8311 (tt0) REVERT: D 44 VAL cc_start: 0.9512 (t) cc_final: 0.9259 (p) REVERT: D 68 ASP cc_start: 0.8581 (t70) cc_final: 0.8328 (t0) REVERT: D 82 HIS cc_start: 0.8612 (t70) cc_final: 0.8378 (t70) REVERT: D 89 ILE cc_start: 0.8912 (mt) cc_final: 0.8513 (tt) REVERT: D 100 LEU cc_start: 0.8926 (mm) cc_final: 0.8715 (mm) REVERT: E 54 TYR cc_start: 0.8080 (m-10) cc_final: 0.7515 (m-80) REVERT: E 82 LEU cc_start: 0.8067 (pt) cc_final: 0.7744 (pt) REVERT: E 93 GLN cc_start: 0.8631 (tt0) cc_final: 0.7919 (tp40) REVERT: F 60 VAL cc_start: 0.9262 (t) cc_final: 0.8027 (t) REVERT: F 63 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8881 (mt-10) REVERT: F 79 LYS cc_start: 0.7279 (mmtt) cc_final: 0.6532 (mmtt) REVERT: F 85 ASP cc_start: 0.8313 (m-30) cc_final: 0.7981 (m-30) REVERT: F 88 TYR cc_start: 0.8753 (m-80) cc_final: 0.8417 (m-80) REVERT: F 93 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8669 (tm-30) REVERT: G 38 ASN cc_start: 0.8925 (m110) cc_final: 0.8686 (m110) REVERT: G 68 ASN cc_start: 0.9231 (m110) cc_final: 0.8855 (m-40) REVERT: G 95 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7780 (tmtt) REVERT: H 37 TYR cc_start: 0.8920 (m-80) cc_final: 0.8000 (m-80) REVERT: H 59 MET cc_start: 0.9191 (tpp) cc_final: 0.8848 (tpp) REVERT: H 68 ASP cc_start: 0.8627 (t0) cc_final: 0.8412 (t0) REVERT: H 113 GLU cc_start: 0.8740 (mp0) cc_final: 0.8456 (mp0) REVERT: K 103 LEU cc_start: 0.9253 (mt) cc_final: 0.9036 (mt) REVERT: K 107 THR cc_start: 0.9223 (p) cc_final: 0.8481 (p) REVERT: K 123 ASP cc_start: 0.8487 (m-30) cc_final: 0.7735 (t70) REVERT: M 49 VAL cc_start: 0.7755 (t) cc_final: 0.7470 (p) REVERT: M 55 LEU cc_start: 0.9119 (mt) cc_final: 0.8832 (mt) REVERT: M 64 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8368 (tm-30) REVERT: M 68 ASN cc_start: 0.9294 (m110) cc_final: 0.9068 (m110) REVERT: N 54 ILE cc_start: 0.7138 (pt) cc_final: 0.6896 (pt) REVERT: N 71 GLU cc_start: 0.8658 (pp20) cc_final: 0.8244 (pp20) REVERT: N 102 LEU cc_start: 0.8117 (mp) cc_final: 0.7878 (tp) REVERT: N 106 LEU cc_start: 0.9472 (mt) cc_final: 0.9233 (mt) REVERT: O 76 GLN cc_start: 0.8791 (tt0) cc_final: 0.8343 (tp40) REVERT: O 80 THR cc_start: 0.7254 (p) cc_final: 0.6961 (t) REVERT: O 96 CYS cc_start: 0.9449 (m) cc_final: 0.9121 (m) REVERT: O 101 VAL cc_start: 0.9502 (m) cc_final: 0.8997 (p) REVERT: O 105 GLU cc_start: 0.9314 (pt0) cc_final: 0.9064 (pt0) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1227 time to fit residues: 67.3912 Evaluate side-chains 276 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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: 0.8980 chunk 151 optimal weight: 9.9990 chunk 94 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 40.0000 chunk 141 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 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 = 0.3719 r_free = 0.3719 target = 0.073465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.051171 restraints weight = 123205.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.052584 restraints weight = 61368.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053493 restraints weight = 39327.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.054065 restraints weight = 30063.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.054361 restraints weight = 25761.644| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21551 Z= 0.238 Angle : 0.797 9.618 31255 Z= 0.448 Chirality : 0.050 0.329 3561 Planarity : 0.006 0.073 2220 Dihedral : 33.409 177.752 6852 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.22), residues: 1219 helix: 0.60 (0.16), residues: 929 sheet: None (None), residues: 0 loop : -0.94 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 52 TYR 0.058 0.003 TYR N 83 PHE 0.019 0.003 PHE B 61 HIS 0.012 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.24 (21551) covalent geometry : angle 0.79664 / 0.45 (31255) hydrogen bonds : bond 0.07477 / 4.99 ( 1312) hydrogen bonds : angle 4.26026 / 3.16 ( 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 342 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.508 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: 0.8479 (m-80) cc_final: 0.8083 (m-10) REVERT: A 110 CYS cc_start: 0.9299 (m) cc_final: 0.9011 (t) REVERT: A 120 MET cc_start: 0.9072 (mtm) cc_final: 0.8821 (mtp) REVERT: B 44 LYS cc_start: 0.8121 (tttm) cc_final: 0.7425 (tttt) REVERT: B 52 GLU cc_start: 0.8320 (mp0) cc_final: 0.8016 (mp0) REVERT: B 63 GLU cc_start: 0.8439 (pp20) cc_final: 0.8214 (tm-30) REVERT: B 74 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7790 (tm-30) REVERT: B 85 ASP cc_start: 0.8503 (m-30) cc_final: 0.8025 (m-30) REVERT: B 98 TYR cc_start: 0.8799 (m-10) cc_final: 0.8372 (m-80) REVERT: C 56 GLU cc_start: 0.8612 (tt0) cc_final: 0.8298 (tt0) REVERT: C 110 ASN cc_start: 0.9005 (t0) cc_final: 0.8534 (m110) REVERT: C 112 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7737 (mm-40) REVERT: D 44 VAL cc_start: 0.9532 (t) cc_final: 0.9272 (p) REVERT: D 68 ASP cc_start: 0.8490 (t70) cc_final: 0.8228 (t0) REVERT: D 82 HIS cc_start: 0.8523 (t70) cc_final: 0.8320 (t70) REVERT: D 89 ILE cc_start: 0.8908 (mt) cc_final: 0.8517 (tt) REVERT: D 96 THR cc_start: 0.9296 (t) cc_final: 0.9024 (p) REVERT: D 100 LEU cc_start: 0.9116 (mm) cc_final: 0.8853 (mm) REVERT: E 54 TYR cc_start: 0.8331 (m-10) cc_final: 0.7557 (m-80) REVERT: E 93 GLN cc_start: 0.8718 (tt0) cc_final: 0.7452 (tp40) REVERT: E 94 GLU cc_start: 0.8855 (tt0) cc_final: 0.8451 (tt0) REVERT: E 97 GLU cc_start: 0.8516 (pm20) cc_final: 0.7890 (pm20) REVERT: F 79 LYS cc_start: 0.7258 (mmtt) cc_final: 0.6977 (tptt) REVERT: F 85 ASP cc_start: 0.8285 (m-30) cc_final: 0.8002 (m-30) REVERT: F 88 TYR cc_start: 0.8211 (m-80) cc_final: 0.7712 (m-80) REVERT: G 38 ASN cc_start: 0.8939 (m110) cc_final: 0.8415 (t0) REVERT: G 68 ASN cc_start: 0.9224 (m110) cc_final: 0.8822 (m-40) REVERT: G 95 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7927 (tmtt) REVERT: H 37 TYR cc_start: 0.8765 (m-80) cc_final: 0.7839 (m-10) REVERT: H 59 MET cc_start: 0.9078 (tpp) cc_final: 0.8684 (tpp) REVERT: K 67 PHE cc_start: 0.8477 (t80) cc_final: 0.8253 (t80) REVERT: K 103 LEU cc_start: 0.9270 (mt) cc_final: 0.9019 (mt) REVERT: K 107 THR cc_start: 0.9182 (p) cc_final: 0.8497 (p) REVERT: K 123 ASP cc_start: 0.8595 (m-30) cc_final: 0.7830 (t0) REVERT: M 49 VAL cc_start: 0.7588 (t) cc_final: 0.7278 (p) REVERT: M 64 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8364 (tm-30) REVERT: N 102 LEU cc_start: 0.8154 (mp) cc_final: 0.7912 (tp) REVERT: O 76 GLN cc_start: 0.8780 (tt0) cc_final: 0.8317 (tp40) REVERT: O 96 CYS cc_start: 0.9426 (m) cc_final: 0.9099 (m) REVERT: O 101 VAL cc_start: 0.9491 (m) cc_final: 0.9015 (p) REVERT: O 105 GLU cc_start: 0.9327 (pt0) cc_final: 0.9057 (pt0) REVERT: O 120 MET cc_start: 0.8776 (ttt) cc_final: 0.8505 (ttt) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1235 time to fit residues: 67.7497 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 : 0.431 ------------------------------------------------------------------------------- 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: 2.9990 chunk 103 optimal weight: 50.0000 chunk 153 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 95 optimal weight: 50.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN 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 108 ASN M 82 HIS P 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.073173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051527 restraints weight = 118617.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.052979 restraints weight = 57826.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.053885 restraints weight = 36559.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.054469 restraints weight = 27581.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.054784 restraints weight = 23324.440| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5947 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= 0.205 Angle : 0.769 8.733 31255 Z= 0.435 Chirality : 0.049 0.317 3561 Planarity : 0.006 0.064 2220 Dihedral : 33.331 175.068 6852 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.19 % Allowed : 0.29 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1219 helix: 0.72 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -0.92 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 42 TYR 0.042 0.003 TYR M 57 PHE 0.042 0.003 PHE D 65 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.21 (21551) covalent geometry : angle 0.76851 / 0.43 (31255) hydrogen bonds : bond 0.06702 / 4.46 ( 1312) hydrogen bonds : angle 4.10232 / 3.05 ( 3284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.91 seconds wall clock time: 58 minutes 48.34 seconds (3528.34 seconds total)