Starting phenix.real_space_refine on Sun Aug 24 11:22:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3f_38880/08_2025/8y3f_38880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3f_38880/08_2025/8y3f_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_2025/8y3f_38880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3f_38880/08_2025/8y3f_38880.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y3f_38880/08_2025/8y3f_38880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3f_38880/08_2025/8y3f_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-2.0-5787/lib/python3.9/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: 4.55, per 1000 atoms: 0.23 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: 1.82 Conformation dependent library (CDL) restraints added in 464.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.55 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: 4.14 Time building geometry restraints manager: 2.44 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=" N ASN M 73 " pdb=" CA ASN M 73 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.24e+00 bond pdb=" N ARG P 36 " pdb=" CA ARG P 36 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.55e+00 bond pdb=" N ARG E 129 " pdb=" CA ARG E 129 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.12e+00 bond pdb=" CG1 ILE A 112 " pdb=" CD1 ILE A 112 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.31e+00 bond pdb=" C3' DG I 159 " pdb=" O3' DG I 159 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.11e+00 ... (remaining 21546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 30335 2.05 - 4.10: 828 4.10 - 6.15: 71 6.15 - 8.20: 17 8.20 - 10.25: 4 Bond angle restraints: 31255 Sorted by residual: angle pdb=" CA ASP N 51 " pdb=" CB ASP N 51 " pdb=" CG ASP N 51 " ideal model delta sigma weight residual 112.60 116.53 -3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" CG ARG G 35 " pdb=" CD ARG G 35 " pdb=" NE ARG G 35 " ideal model delta sigma weight residual 112.00 120.08 -8.08 2.20e+00 2.07e-01 1.35e+01 angle pdb=" CA GLN M 104 " pdb=" CB GLN M 104 " pdb=" CG GLN M 104 " ideal model delta sigma weight residual 114.10 121.38 -7.28 2.00e+00 2.50e-01 1.33e+01 angle pdb=" N ARG P 78 " pdb=" CA ARG P 78 " pdb=" C ARG P 78 " ideal model delta sigma weight residual 110.14 104.54 5.60 1.55e+00 4.16e-01 1.31e+01 angle pdb=" CG ARG O 69 " pdb=" CD ARG O 69 " pdb=" NE ARG O 69 " ideal model delta sigma weight residual 112.00 119.88 -7.88 2.20e+00 2.07e-01 1.28e+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: 3012 0.051 - 0.102: 460 0.102 - 0.153: 71 0.153 - 0.204: 15 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=" 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 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 2.35 -2.56 -0.21 2.00e-01 2.50e+01 1.10e+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: 0.360 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: 0.060 Set scattering table: 0.060 Process input model: 21.680 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 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 : 0.004 0.059 21551 Z= 0.198 Angle : 0.746 10.253 31255 Z= 0.449 Chirality : 0.039 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 aren 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 covalent geometry : bond 0.00414 (21551) covalent geometry : angle 0.74559 (31255) hydrogen bonds : bond 0.10958 ( 1312) hydrogen bonds : angle 4.51121 ( 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 : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PRO cc_start: 0.7798 (Cg_exo) cc_final: 0.7595 (Cg_endo) REVERT: A 61 LEU cc_start: 0.8725 (mt) cc_final: 0.8175 (mp) REVERT: A 84 PHE cc_start: 0.7753 (m-80) cc_final: 0.7509 (m-10) REVERT: A 89 VAL cc_start: 0.9378 (t) cc_final: 0.9170 (p) REVERT: A 92 LEU cc_start: 0.9424 (mt) cc_final: 0.8843 (mt) REVERT: A 93 GLN cc_start: 0.8689 (tt0) cc_final: 0.8324 (tp40) REVERT: A 108 ASN cc_start: 0.8749 (t0) cc_final: 0.8122 (t0) REVERT: B 90 LEU cc_start: 0.9103 (mt) cc_final: 0.8697 (mp) REVERT: B 96 THR cc_start: 0.8661 (p) cc_final: 0.8297 (t) REVERT: C 25 PHE cc_start: 0.8607 (m-80) cc_final: 0.8381 (m-10) REVERT: C 26 PRO cc_start: 0.8556 (Cg_endo) cc_final: 0.8307 (Cg_exo) REVERT: C 78 ILE cc_start: 0.8793 (mm) cc_final: 0.8590 (mm) REVERT: C 91 GLU cc_start: 0.8521 (pm20) cc_final: 0.8174 (pp20) REVERT: C 110 ASN cc_start: 0.8874 (t0) cc_final: 0.8386 (t0) REVERT: D 34 LYS cc_start: 0.7417 (tptp) cc_final: 0.7059 (tppt) REVERT: D 42 TYR cc_start: 0.7662 (t80) cc_final: 0.7372 (t80) REVERT: D 100 LEU cc_start: 0.9272 (mp) cc_final: 0.8717 (mm) REVERT: E 60 LEU cc_start: 0.9028 (mt) cc_final: 0.8488 (mp) REVERT: E 93 GLN cc_start: 0.9290 (tt0) cc_final: 0.8205 (tp-100) REVERT: E 101 VAL cc_start: 0.9409 (m) cc_final: 0.9156 (p) REVERT: E 106 ASP cc_start: 0.8221 (m-30) cc_final: 0.7938 (m-30) REVERT: E 107 THR cc_start: 0.9172 (m) cc_final: 0.8616 (p) REVERT: F 25 ASN cc_start: 0.7342 (m-40) cc_final: 0.6497 (m-40) REVERT: F 49 LEU cc_start: 0.7418 (mp) cc_final: 0.6823 (mt) REVERT: F 59 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8389 (tttt) REVERT: F 85 ASP cc_start: 0.8698 (m-30) cc_final: 0.8139 (m-30) REVERT: G 35 ARG cc_start: 0.7430 (mtm180) cc_final: 0.7185 (ptp90) REVERT: H 37 TYR cc_start: 0.8047 (m-80) cc_final: 0.7623 (m-80) REVERT: H 42 TYR cc_start: 0.7127 (t80) cc_final: 0.6857 (t80) REVERT: H 45 LEU cc_start: 0.7677 (tp) cc_final: 0.7385 (tp) REVERT: H 57 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7832 (mmmt) REVERT: H 59 MET cc_start: 0.8299 (tpp) cc_final: 0.7818 (mmm) REVERT: H 61 ILE cc_start: 0.9130 (mt) cc_final: 0.8748 (mm) REVERT: H 65 PHE cc_start: 0.8710 (t80) cc_final: 0.8290 (t80) REVERT: H 68 ASP cc_start: 0.6642 (t0) cc_final: 0.5851 (t0) REVERT: H 71 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6787 (mt-10) REVERT: H 101 LEU cc_start: 0.8643 (mp) cc_final: 0.8383 (mt) REVERT: L 30 THR cc_start: 0.7324 (p) cc_final: 0.6905 (t) REVERT: L 86 VAL cc_start: 0.4849 (t) cc_final: 0.4545 (t) REVERT: L 87 VAL cc_start: 0.7019 (t) cc_final: 0.6548 (p) REVERT: L 88 TYR cc_start: 0.2709 (m-10) cc_final: 0.2143 (m-10) REVERT: N 41 VAL cc_start: 0.8862 (t) cc_final: 0.8607 (t) REVERT: N 54 ILE cc_start: 0.6873 (tt) cc_final: 0.6551 (pt) REVERT: N 62 MET cc_start: 0.7795 (mmm) cc_final: 0.7350 (mmp) REVERT: N 68 ASP cc_start: 0.7005 (t70) cc_final: 0.6660 (t0) REVERT: O 61 LEU cc_start: 0.8036 (mt) cc_final: 0.7542 (mt) REVERT: O 74 ILE cc_start: 0.8047 (tp) cc_final: 0.7792 (mm) REVERT: O 76 GLN cc_start: 0.8229 (tt0) cc_final: 0.7906 (tp40) REVERT: O 92 LEU cc_start: 0.8472 (mm) cc_final: 0.8143 (mm) REVERT: O 103 LEU cc_start: 0.8743 (tp) cc_final: 0.8488 (tt) REVERT: P 93 GLN cc_start: 0.8772 (tt0) cc_final: 0.8447 (tm-30) outliers start: 0 outliers final: 0 residues processed: 592 average time/residue: 0.1968 time to fit residues: 164.4381 Evaluate side-chains 378 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 108 ASN C 24 GLN C 38 ASN D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 27 GLN M 68 ASN ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN N 109 HIS ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.082290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.060505 restraints weight = 124527.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.061711 restraints weight = 68927.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.062585 restraints weight = 43268.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063181 restraints weight = 32672.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.063167 restraints weight = 30590.904| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 21551 Z= 0.280 Angle : 0.733 13.180 31255 Z= 0.425 Chirality : 0.040 0.225 3561 Planarity : 0.007 0.102 2220 Dihedral : 32.820 178.481 6852 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.57 % Allowed : 5.93 % Favored : 93.50 % 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 aren not related in a simple way. whole: 1.32 (0.22), residues: 1219 helix: 1.25 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -0.12 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 52 TYR 0.044 0.003 TYR B 88 PHE 0.016 0.003 PHE N 65 HIS 0.012 0.003 HIS M 82 Details of bonding type rmsd covalent geometry : bond 0.00600 (21551) covalent geometry : angle 0.73264 (31255) hydrogen bonds : bond 0.07001 ( 1312) hydrogen bonds : angle 4.02607 ( 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 428 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 422 time to evaluate : 0.561 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 76 GLN cc_start: 0.8606 (tp40) cc_final: 0.8309 (tp40) REVERT: A 84 PHE cc_start: 0.8428 (m-80) cc_final: 0.8215 (m-10) REVERT: A 110 CYS cc_start: 0.9198 (m) cc_final: 0.8961 (m) REVERT: A 120 MET cc_start: 0.9156 (mtm) cc_final: 0.8863 (mtp) REVERT: B 45 ARG cc_start: 0.7476 (mtp85) cc_final: 0.7227 (tpt-90) REVERT: B 74 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7866 (tm-30) REVERT: B 88 TYR cc_start: 0.8088 (m-10) cc_final: 0.6509 (m-80) REVERT: B 98 TYR cc_start: 0.8760 (m-10) cc_final: 0.8488 (m-10) REVERT: C 25 PHE cc_start: 0.8557 (m-80) cc_final: 0.7762 (m-10) REVERT: C 35 ARG cc_start: 0.8962 (mtt90) cc_final: 0.8561 (mmt180) REVERT: C 38 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8584 (t0) REVERT: C 102 ILE cc_start: 0.8786 (mm) cc_final: 0.8443 (tt) REVERT: C 104 GLN cc_start: 0.8332 (mt0) cc_final: 0.7840 (mt0) REVERT: C 110 ASN cc_start: 0.9140 (t0) cc_final: 0.8685 (m110) REVERT: D 34 LYS cc_start: 0.7583 (tptp) cc_final: 0.7275 (tppt) REVERT: D 44 VAL cc_start: 0.9448 (t) cc_final: 0.9097 (p) REVERT: D 68 ASP cc_start: 0.8467 (t70) cc_final: 0.8202 (t0) REVERT: D 82 HIS cc_start: 0.8219 (t-90) cc_final: 0.7853 (t70) REVERT: D 95 GLN cc_start: 0.8512 (tt0) cc_final: 0.8166 (tt0) REVERT: E 46 VAL cc_start: 0.7904 (t) cc_final: 0.7614 (t) REVERT: E 82 LEU cc_start: 0.7049 (pt) cc_final: 0.6849 (pt) REVERT: E 93 GLN cc_start: 0.8948 (tt0) cc_final: 0.7941 (tp40) REVERT: E 106 ASP cc_start: 0.8689 (m-30) cc_final: 0.8356 (m-30) REVERT: F 25 ASN cc_start: 0.7641 (m-40) cc_final: 0.7274 (m110) REVERT: F 44 LYS cc_start: 0.8673 (ttpp) cc_final: 0.7964 (mtpt) REVERT: F 64 ASN cc_start: 0.8837 (m110) cc_final: 0.8506 (m110) REVERT: F 79 LYS cc_start: 0.7396 (mmtt) cc_final: 0.6865 (tptp) REVERT: F 88 TYR cc_start: 0.8696 (m-80) cc_final: 0.8188 (m-80) REVERT: G 35 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7429 (mtm110) REVERT: G 38 ASN cc_start: 0.8276 (m110) cc_final: 0.7781 (m110) REVERT: G 68 ASN cc_start: 0.9224 (m110) cc_final: 0.8956 (m-40) REVERT: G 95 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7818 (tmtt) REVERT: H 37 TYR cc_start: 0.8863 (m-80) cc_final: 0.7722 (m-80) REVERT: H 68 ASP cc_start: 0.8685 (t0) cc_final: 0.8044 (t0) REVERT: H 94 ILE cc_start: 0.9494 (mm) cc_final: 0.9272 (mm) REVERT: H 106 LEU cc_start: 0.9627 (mt) cc_final: 0.9019 (mt) REVERT: H 112 SER cc_start: 0.9144 (t) cc_final: 0.8844 (p) REVERT: L 62 LEU cc_start: 0.9732 (mm) cc_final: 0.9486 (mm) REVERT: L 85 ASP cc_start: 0.5405 (m-30) cc_final: 0.4915 (m-30) REVERT: M 25 PHE cc_start: 0.7367 (m-10) cc_final: 0.6636 (m-10) REVERT: M 56 GLU cc_start: 0.8044 (tt0) cc_final: 0.6863 (tt0) REVERT: M 58 LEU cc_start: 0.8986 (mp) cc_final: 0.8742 (pp) REVERT: M 64 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8109 (tm-30) REVERT: M 84 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8582 (tm-30) REVERT: M 107 VAL cc_start: 0.8932 (t) cc_final: 0.8661 (p) REVERT: N 68 ASP cc_start: 0.8613 (t70) cc_final: 0.8171 (t0) REVERT: N 71 GLU cc_start: 0.8678 (pp20) cc_final: 0.8236 (pp20) REVERT: N 105 GLU cc_start: 0.8839 (pm20) cc_final: 0.8599 (pt0) REVERT: O 41 TYR cc_start: 0.6081 (m-80) cc_final: 0.5616 (m-80) REVERT: O 60 LEU cc_start: 0.5540 (mp) cc_final: 0.4475 (mp) REVERT: O 62 ILE cc_start: 0.8193 (tp) cc_final: 0.7931 (pt) REVERT: O 64 LYS cc_start: 0.8078 (ptmm) cc_final: 0.7725 (pptt) REVERT: O 65 LEU cc_start: 0.8180 (tp) cc_final: 0.7663 (tp) REVERT: O 68 GLN cc_start: 0.9130 (mt0) cc_final: 0.8798 (mt0) REVERT: O 76 GLN cc_start: 0.9096 (tt0) cc_final: 0.8629 (tp40) REVERT: O 90 MET cc_start: 0.9028 (mtm) cc_final: 0.8464 (ptm) REVERT: O 96 CYS cc_start: 0.9475 (m) cc_final: 0.9190 (m) REVERT: O 105 GLU cc_start: 0.9307 (pt0) cc_final: 0.8999 (pt0) REVERT: P 57 VAL cc_start: 0.9306 (t) cc_final: 0.9069 (p) REVERT: P 84 MET cc_start: 0.7054 (tpp) cc_final: 0.6695 (tpp) REVERT: P 93 GLN cc_start: 0.8743 (tt0) cc_final: 0.8199 (tm-30) outliers start: 6 outliers final: 0 residues processed: 426 average time/residue: 0.1598 time to fit residues: 102.8982 Evaluate side-chains 307 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 110 ASN E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.075858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053892 restraints weight = 117594.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.055409 restraints weight = 57536.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.056409 restraints weight = 36019.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.057040 restraints weight = 26745.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.057393 restraints weight = 22367.930| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-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: 5 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21551 Z= 0.189 Angle : 0.637 7.706 31255 Z= 0.373 Chirality : 0.037 0.202 3561 Planarity : 0.005 0.056 2220 Dihedral : 32.723 177.596 6852 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.38 % Allowed : 4.88 % Favored : 94.74 % 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 aren not related in a simple way. whole: 1.64 (0.22), residues: 1219 helix: 1.50 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -0.08 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 63 TYR 0.022 0.002 TYR B 88 PHE 0.018 0.002 PHE N 65 HIS 0.009 0.002 HIS M 82 Details of bonding type rmsd covalent geometry : bond 0.00413 (21551) covalent geometry : angle 0.63707 (31255) hydrogen bonds : bond 0.05207 ( 1312) hydrogen bonds : angle 3.61650 ( 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 401 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 397 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8402 (m-80) cc_final: 0.7988 (m-10) REVERT: A 93 GLN cc_start: 0.9200 (tt0) cc_final: 0.8520 (tp40) REVERT: A 108 ASN cc_start: 0.8769 (t0) cc_final: 0.8566 (t0) REVERT: A 110 CYS cc_start: 0.9242 (m) cc_final: 0.8942 (m) REVERT: A 120 MET cc_start: 0.9261 (mtm) cc_final: 0.8887 (mtp) REVERT: B 52 GLU cc_start: 0.8674 (mp0) cc_final: 0.8333 (mp0) REVERT: B 63 GLU cc_start: 0.8770 (tt0) cc_final: 0.7992 (tt0) REVERT: B 68 ASP cc_start: 0.9037 (m-30) cc_final: 0.8799 (m-30) REVERT: B 74 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 88 TYR cc_start: 0.7786 (m-10) cc_final: 0.7394 (m-80) REVERT: B 98 TYR cc_start: 0.8904 (m-10) cc_final: 0.8366 (m-10) REVERT: B 100 PHE cc_start: 0.8413 (m-80) cc_final: 0.8071 (m-10) REVERT: C 35 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8612 (mmt-90) REVERT: C 39 TYR cc_start: 0.9082 (m-80) cc_final: 0.8272 (m-80) REVERT: C 104 GLN cc_start: 0.8365 (mt0) cc_final: 0.7635 (mm-40) REVERT: D 37 TYR cc_start: 0.9295 (m-80) cc_final: 0.8923 (m-10) REVERT: D 44 VAL cc_start: 0.9368 (t) cc_final: 0.9010 (p) REVERT: D 62 MET cc_start: 0.8513 (mmm) cc_final: 0.8196 (mmp) REVERT: D 82 HIS cc_start: 0.8411 (t-90) cc_final: 0.8210 (t70) REVERT: D 89 ILE cc_start: 0.8783 (mt) cc_final: 0.8390 (tt) REVERT: D 100 LEU cc_start: 0.9117 (mm) cc_final: 0.8889 (mm) REVERT: D 108 LYS cc_start: 0.9198 (mttm) cc_final: 0.8915 (mtpt) REVERT: E 67 PHE cc_start: 0.7982 (t80) cc_final: 0.7764 (t80) REVERT: E 81 ASP cc_start: 0.7597 (t0) cc_final: 0.7287 (t0) REVERT: E 90 MET cc_start: 0.9034 (mmm) cc_final: 0.8389 (tpp) REVERT: E 93 GLN cc_start: 0.9038 (tt0) cc_final: 0.8176 (tt0) REVERT: E 103 LEU cc_start: 0.9330 (tt) cc_final: 0.9123 (tt) REVERT: E 107 THR cc_start: 0.9247 (m) cc_final: 0.8967 (p) REVERT: E 109 LEU cc_start: 0.9114 (mp) cc_final: 0.8571 (mt) REVERT: F 25 ASN cc_start: 0.8069 (m-40) cc_final: 0.7666 (m110) REVERT: F 44 LYS cc_start: 0.8503 (ttpp) cc_final: 0.7381 (mtpp) REVERT: F 79 LYS cc_start: 0.7359 (mmtt) cc_final: 0.6712 (tptp) REVERT: F 88 TYR cc_start: 0.8544 (m-10) cc_final: 0.8337 (m-80) REVERT: G 35 ARG cc_start: 0.8200 (mtm180) cc_final: 0.7608 (ptp90) REVERT: G 38 ASN cc_start: 0.8292 (m110) cc_final: 0.7834 (t0) REVERT: G 42 ARG cc_start: 0.8262 (ptm160) cc_final: 0.7993 (ptm160) REVERT: G 68 ASN cc_start: 0.9182 (m110) cc_final: 0.8902 (m-40) REVERT: G 95 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7650 (tmtt) REVERT: H 37 TYR cc_start: 0.8945 (m-80) cc_final: 0.7728 (m-80) REVERT: H 40 TYR cc_start: 0.8869 (m-80) cc_final: 0.7968 (m-10) REVERT: H 68 ASP cc_start: 0.8780 (t0) cc_final: 0.7957 (t0) REVERT: H 94 ILE cc_start: 0.9421 (mm) cc_final: 0.9219 (mm) REVERT: H 112 SER cc_start: 0.9192 (t) cc_final: 0.8865 (p) REVERT: K 97 GLU cc_start: 0.8827 (mp0) cc_final: 0.8621 (mp0) REVERT: K 103 LEU cc_start: 0.9282 (mt) cc_final: 0.8995 (mt) REVERT: K 120 MET cc_start: 0.5268 (mtt) cc_final: 0.4965 (mtp) REVERT: L 30 THR cc_start: 0.7260 (p) cc_final: 0.7013 (p) REVERT: L 62 LEU cc_start: 0.9712 (mm) cc_final: 0.9459 (mm) REVERT: M 25 PHE cc_start: 0.7522 (m-10) cc_final: 0.6744 (m-10) REVERT: M 56 GLU cc_start: 0.8161 (tt0) cc_final: 0.7094 (tt0) REVERT: M 64 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8150 (tm-30) REVERT: M 84 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8538 (tm-30) REVERT: M 107 VAL cc_start: 0.9017 (t) cc_final: 0.8775 (p) REVERT: N 76 GLU cc_start: 0.7529 (tp30) cc_final: 0.7173 (tp30) REVERT: O 53 ARG cc_start: 0.9314 (tpp-160) cc_final: 0.8981 (ptm-80) REVERT: O 54 TYR cc_start: 0.8989 (m-80) cc_final: 0.8464 (m-80) REVERT: O 60 LEU cc_start: 0.6552 (mp) cc_final: 0.5634 (mm) REVERT: O 65 LEU cc_start: 0.8337 (tp) cc_final: 0.7861 (tp) REVERT: O 67 PHE cc_start: 0.8807 (t80) cc_final: 0.8466 (t80) REVERT: O 76 GLN cc_start: 0.9085 (tt0) cc_final: 0.8598 (tp40) REVERT: O 96 CYS cc_start: 0.9466 (m) cc_final: 0.9100 (m) REVERT: O 101 VAL cc_start: 0.9413 (m) cc_final: 0.8838 (p) REVERT: O 105 GLU cc_start: 0.9250 (pt0) cc_final: 0.8933 (pt0) REVERT: P 93 GLN cc_start: 0.8398 (tt0) cc_final: 0.7959 (tm-30) REVERT: P 100 PHE cc_start: 0.8492 (m-10) cc_final: 0.8264 (m-10) outliers start: 4 outliers final: 0 residues processed: 399 average time/residue: 0.1489 time to fit residues: 92.2164 Evaluate side-chains 315 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 134 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** 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 = 0.3748 r_free = 0.3748 target = 0.075196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.052640 restraints weight = 123563.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.054112 restraints weight = 62195.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055072 restraints weight = 39918.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.055672 restraints weight = 30328.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.055978 restraints weight = 25832.725| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21551 Z= 0.207 Angle : 0.645 10.173 31255 Z= 0.378 Chirality : 0.037 0.182 3561 Planarity : 0.005 0.050 2220 Dihedral : 32.864 178.981 6852 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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 aren not related in a simple way. whole: 1.44 (0.22), residues: 1219 helix: 1.37 (0.16), residues: 926 sheet: None (None), residues: 0 loop : -0.21 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 92 TYR 0.045 0.002 TYR B 88 PHE 0.019 0.002 PHE N 65 HIS 0.008 0.002 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00453 (21551) covalent geometry : angle 0.64491 (31255) hydrogen bonds : bond 0.05755 ( 1312) hydrogen bonds : angle 3.70062 ( 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 387 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.564 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 57 SER cc_start: 0.8915 (t) cc_final: 0.7874 (p) REVERT: A 76 GLN cc_start: 0.8644 (tp40) cc_final: 0.8418 (tp40) REVERT: A 84 PHE cc_start: 0.8367 (m-80) cc_final: 0.8002 (m-10) REVERT: A 106 ASP cc_start: 0.9056 (m-30) cc_final: 0.8711 (m-30) REVERT: A 107 THR cc_start: 0.8797 (p) cc_final: 0.8492 (t) REVERT: A 110 CYS cc_start: 0.9129 (m) cc_final: 0.8309 (m) REVERT: A 120 MET cc_start: 0.9200 (mtm) cc_final: 0.8854 (mtp) REVERT: B 52 GLU cc_start: 0.8636 (mp0) cc_final: 0.8314 (mp0) REVERT: B 68 ASP cc_start: 0.9024 (m-30) cc_final: 0.8817 (m-30) REVERT: B 74 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 88 TYR cc_start: 0.7398 (m-10) cc_final: 0.7047 (m-80) REVERT: B 98 TYR cc_start: 0.8785 (m-10) cc_final: 0.8188 (m-10) REVERT: C 35 ARG cc_start: 0.8920 (mtt90) cc_final: 0.8657 (mmt180) REVERT: C 39 TYR cc_start: 0.8794 (m-80) cc_final: 0.8134 (m-80) REVERT: C 104 GLN cc_start: 0.8438 (mt0) cc_final: 0.7752 (mm-40) REVERT: C 112 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7937 (mm-40) REVERT: D 42 TYR cc_start: 0.8556 (t80) cc_final: 0.8336 (t80) REVERT: D 44 VAL cc_start: 0.9414 (t) cc_final: 0.9072 (p) REVERT: D 89 ILE cc_start: 0.8570 (mt) cc_final: 0.8250 (tt) REVERT: D 100 LEU cc_start: 0.9124 (mm) cc_final: 0.8870 (mm) REVERT: D 108 LYS cc_start: 0.9235 (mttm) cc_final: 0.8931 (mtmt) REVERT: E 54 TYR cc_start: 0.8487 (m-10) cc_final: 0.7773 (m-80) REVERT: E 81 ASP cc_start: 0.7550 (t0) cc_final: 0.7324 (t0) REVERT: E 82 LEU cc_start: 0.7359 (pt) cc_final: 0.7158 (pt) REVERT: E 107 THR cc_start: 0.9157 (m) cc_final: 0.8927 (m) REVERT: E 109 LEU cc_start: 0.9153 (mp) cc_final: 0.8916 (mt) REVERT: F 25 ASN cc_start: 0.8124 (m-40) cc_final: 0.7691 (m110) REVERT: F 64 ASN cc_start: 0.8911 (m110) cc_final: 0.8543 (m110) REVERT: F 79 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6695 (mmtt) REVERT: G 35 ARG cc_start: 0.8260 (mtm180) cc_final: 0.7544 (ptp90) REVERT: G 38 ASN cc_start: 0.8518 (m110) cc_final: 0.8080 (t0) REVERT: G 68 ASN cc_start: 0.9207 (m110) cc_final: 0.8924 (m-40) REVERT: G 95 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7703 (tmtt) REVERT: H 37 TYR cc_start: 0.8947 (m-80) cc_final: 0.7705 (m-80) REVERT: H 59 MET cc_start: 0.9217 (tpp) cc_final: 0.8838 (tpp) REVERT: H 68 ASP cc_start: 0.8787 (t0) cc_final: 0.8343 (t0) REVERT: H 112 SER cc_start: 0.9122 (t) cc_final: 0.8895 (p) REVERT: K 78 PHE cc_start: 0.7608 (m-80) cc_final: 0.7320 (m-80) REVERT: K 103 LEU cc_start: 0.9318 (mt) cc_final: 0.8971 (mt) REVERT: K 120 MET cc_start: 0.5278 (mtt) cc_final: 0.4998 (mtp) REVERT: M 25 PHE cc_start: 0.7802 (m-10) cc_final: 0.7583 (m-10) REVERT: M 49 VAL cc_start: 0.7636 (t) cc_final: 0.7323 (p) REVERT: M 68 ASN cc_start: 0.9267 (m110) cc_final: 0.9022 (t0) REVERT: M 72 ASP cc_start: 0.7679 (m-30) cc_final: 0.7259 (m-30) REVERT: N 39 ILE cc_start: 0.8081 (tp) cc_final: 0.7873 (tt) REVERT: O 54 TYR cc_start: 0.8981 (m-80) cc_final: 0.8609 (m-10) REVERT: O 64 LYS cc_start: 0.8500 (pptt) cc_final: 0.8206 (pptt) REVERT: O 65 LEU cc_start: 0.8159 (tp) cc_final: 0.7782 (tp) REVERT: O 67 PHE cc_start: 0.8837 (t80) cc_final: 0.8381 (t80) REVERT: O 76 GLN cc_start: 0.9029 (tt0) cc_final: 0.8509 (tp40) REVERT: O 96 CYS cc_start: 0.9354 (m) cc_final: 0.9023 (m) REVERT: O 101 VAL cc_start: 0.9407 (m) cc_final: 0.8872 (p) REVERT: O 105 GLU cc_start: 0.9272 (pt0) cc_final: 0.8960 (pt0) REVERT: P 44 LYS cc_start: 0.7204 (tttt) cc_final: 0.6979 (tptm) REVERT: P 100 PHE cc_start: 0.8000 (m-10) cc_final: 0.7651 (m-10) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1560 time to fit residues: 93.3032 Evaluate side-chains 300 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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: 0.9980 chunk 163 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.073475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051769 restraints weight = 118580.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.053261 restraints weight = 58214.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.054223 restraints weight = 36774.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.054829 restraints weight = 27500.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.055178 restraints weight = 23181.729| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- 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: 5 | |-----------------------------------------------------------------------------| |-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: 5 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21551 Z= 0.227 Angle : 0.667 9.835 31255 Z= 0.389 Chirality : 0.037 0.164 3561 Planarity : 0.005 0.052 2220 Dihedral : 33.100 178.297 6852 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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 aren not related in a simple way. whole: 1.18 (0.22), residues: 1219 helix: 1.20 (0.16), residues: 933 sheet: None (None), residues: 0 loop : -0.41 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 92 TYR 0.046 0.003 TYR N 83 PHE 0.025 0.002 PHE N 65 HIS 0.007 0.002 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00494 (21551) covalent geometry : angle 0.66713 (31255) hydrogen bonds : bond 0.06132 ( 1312) hydrogen bonds : angle 3.82755 ( 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 377 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.673 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: 0.8382 (m-80) cc_final: 0.8047 (m-80) REVERT: A 93 GLN cc_start: 0.8937 (tp40) cc_final: 0.8290 (tp40) REVERT: A 110 CYS cc_start: 0.9188 (m) cc_final: 0.8641 (t) REVERT: A 120 MET cc_start: 0.9245 (mtm) cc_final: 0.8956 (mtp) REVERT: A 123 ASP cc_start: 0.8178 (t0) cc_final: 0.7423 (t70) REVERT: B 37 LEU cc_start: 0.9352 (mm) cc_final: 0.9116 (mm) REVERT: B 45 ARG cc_start: 0.8009 (tpt-90) cc_final: 0.7440 (tpt-90) REVERT: B 52 GLU cc_start: 0.8528 (mp0) cc_final: 0.8222 (mp0) REVERT: B 63 GLU cc_start: 0.8698 (tt0) cc_final: 0.8024 (tm-30) REVERT: B 64 ASN cc_start: 0.9036 (t0) cc_final: 0.8778 (t0) REVERT: B 74 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7962 (tm-30) REVERT: B 84 MET cc_start: 0.8336 (tpt) cc_final: 0.7638 (tpp) REVERT: B 88 TYR cc_start: 0.8144 (m-80) cc_final: 0.7556 (m-80) REVERT: B 98 TYR cc_start: 0.8807 (m-10) cc_final: 0.8382 (m-80) REVERT: C 104 GLN cc_start: 0.8720 (mt0) cc_final: 0.8404 (mt0) REVERT: C 112 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7824 (mm-40) REVERT: D 42 TYR cc_start: 0.8781 (t80) cc_final: 0.8512 (t80) REVERT: D 44 VAL cc_start: 0.9481 (t) cc_final: 0.9237 (p) REVERT: D 68 ASP cc_start: 0.8539 (t70) cc_final: 0.8275 (t0) REVERT: D 89 ILE cc_start: 0.8723 (mt) cc_final: 0.8464 (tt) REVERT: D 105 GLU cc_start: 0.8387 (pm20) cc_final: 0.8175 (pm20) REVERT: E 54 TYR cc_start: 0.8662 (m-10) cc_final: 0.7899 (m-80) REVERT: E 81 ASP cc_start: 0.7567 (t0) cc_final: 0.7258 (t0) REVERT: E 82 LEU cc_start: 0.7796 (pt) cc_final: 0.7494 (pt) REVERT: E 107 THR cc_start: 0.9219 (m) cc_final: 0.8949 (p) REVERT: E 109 LEU cc_start: 0.9056 (mp) cc_final: 0.8757 (mt) REVERT: E 113 HIS cc_start: 0.8929 (t70) cc_final: 0.7942 (t-90) REVERT: F 25 ASN cc_start: 0.8127 (m-40) cc_final: 0.7701 (m110) REVERT: F 44 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8170 (mtpp) REVERT: F 79 LYS cc_start: 0.7370 (mmtt) cc_final: 0.6659 (mmtt) REVERT: G 38 ASN cc_start: 0.8855 (m110) cc_final: 0.8433 (t0) REVERT: G 68 ASN cc_start: 0.9262 (m110) cc_final: 0.8878 (t0) REVERT: G 95 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7916 (tmtt) REVERT: H 37 TYR cc_start: 0.8928 (m-80) cc_final: 0.7792 (m-80) REVERT: H 59 MET cc_start: 0.9238 (tpp) cc_final: 0.8829 (tpp) REVERT: H 68 ASP cc_start: 0.8963 (t0) cc_final: 0.8645 (t0) REVERT: H 112 SER cc_start: 0.9088 (t) cc_final: 0.8823 (p) REVERT: K 67 PHE cc_start: 0.8619 (t80) cc_final: 0.8361 (t80) REVERT: K 103 LEU cc_start: 0.9251 (mt) cc_final: 0.8924 (mt) REVERT: K 120 MET cc_start: 0.5235 (mtt) cc_final: 0.4584 (mtp) REVERT: M 49 VAL cc_start: 0.7840 (t) cc_final: 0.7548 (p) REVERT: M 64 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8266 (tm-30) REVERT: M 84 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8413 (tm-30) REVERT: N 54 ILE cc_start: 0.7102 (tt) cc_final: 0.6867 (tt) REVERT: N 105 GLU cc_start: 0.9108 (pm20) cc_final: 0.8813 (pm20) REVERT: O 54 TYR cc_start: 0.8984 (m-80) cc_final: 0.8607 (m-10) REVERT: O 59 GLU cc_start: 0.8838 (mp0) cc_final: 0.7945 (tm-30) REVERT: O 60 LEU cc_start: 0.8027 (mp) cc_final: 0.7393 (mt) REVERT: O 64 LYS cc_start: 0.8506 (pptt) cc_final: 0.8224 (pptt) REVERT: O 65 LEU cc_start: 0.8241 (tp) cc_final: 0.7804 (tp) REVERT: O 67 PHE cc_start: 0.8869 (t80) cc_final: 0.8592 (t80) REVERT: O 74 ILE cc_start: 0.8945 (tp) cc_final: 0.8503 (tp) REVERT: O 76 GLN cc_start: 0.9080 (tt0) cc_final: 0.8670 (tp40) REVERT: O 90 MET cc_start: 0.8858 (mtt) cc_final: 0.8486 (ptm) REVERT: O 96 CYS cc_start: 0.9538 (m) cc_final: 0.9187 (m) REVERT: O 97 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8599 (mp0) REVERT: O 101 VAL cc_start: 0.9455 (m) cc_final: 0.8926 (p) REVERT: O 105 GLU cc_start: 0.9294 (pt0) cc_final: 0.9019 (pt0) REVERT: P 44 LYS cc_start: 0.7247 (tttt) cc_final: 0.6890 (tptm) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.1502 time to fit residues: 88.3520 Evaluate side-chains 303 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 7.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 166 optimal weight: 0.1980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** 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** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.075821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054219 restraints weight = 115713.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.055783 restraints weight = 55655.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.056777 restraints weight = 34766.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.057412 restraints weight = 25930.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.057784 restraints weight = 21804.505| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21551 Z= 0.159 Angle : 0.627 8.294 31255 Z= 0.365 Chirality : 0.036 0.208 3561 Planarity : 0.005 0.066 2220 Dihedral : 32.801 178.104 6852 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.19 % Allowed : 2.01 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.23), residues: 1219 helix: 1.38 (0.16), residues: 932 sheet: None (None), residues: 0 loop : -0.43 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 42 TYR 0.023 0.002 TYR G 57 PHE 0.018 0.002 PHE N 65 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00343 (21551) covalent geometry : angle 0.62692 (31255) hydrogen bonds : bond 0.04741 ( 1312) hydrogen bonds : angle 3.48718 ( 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 394 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 392 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8193 (m-80) cc_final: 0.7922 (m-80) REVERT: A 93 GLN cc_start: 0.8987 (tp40) cc_final: 0.8489 (tp40) REVERT: A 105 GLU cc_start: 0.7372 (pp20) cc_final: 0.6871 (pp20) REVERT: A 106 ASP cc_start: 0.8943 (m-30) cc_final: 0.8054 (m-30) REVERT: A 110 CYS cc_start: 0.9134 (m) cc_final: 0.8515 (t) REVERT: A 123 ASP cc_start: 0.7539 (t0) cc_final: 0.7139 (t70) REVERT: B 45 ARG cc_start: 0.8018 (tpt-90) cc_final: 0.7474 (tpt-90) REVERT: B 52 GLU cc_start: 0.8650 (mp0) cc_final: 0.8365 (mp0) REVERT: B 63 GLU cc_start: 0.8570 (tt0) cc_final: 0.7919 (tm-30) REVERT: B 64 ASN cc_start: 0.8957 (t0) cc_final: 0.8730 (t0) REVERT: B 74 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7878 (tm-30) REVERT: B 84 MET cc_start: 0.8270 (tpt) cc_final: 0.7409 (tpp) REVERT: B 88 TYR cc_start: 0.7887 (m-80) cc_final: 0.7484 (m-80) REVERT: B 98 TYR cc_start: 0.8906 (m-10) cc_final: 0.8333 (m-10) REVERT: C 112 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7694 (mm-40) REVERT: D 44 VAL cc_start: 0.9414 (t) cc_final: 0.9063 (p) REVERT: D 62 MET cc_start: 0.8660 (mmm) cc_final: 0.8145 (mmp) REVERT: D 65 PHE cc_start: 0.8655 (t80) cc_final: 0.8435 (t80) REVERT: D 68 ASP cc_start: 0.8429 (t70) cc_final: 0.8153 (t0) REVERT: D 83 TYR cc_start: 0.8588 (t80) cc_final: 0.7646 (t80) REVERT: E 54 TYR cc_start: 0.8519 (m-10) cc_final: 0.7738 (m-80) REVERT: E 81 ASP cc_start: 0.7569 (t0) cc_final: 0.7322 (t0) REVERT: E 82 LEU cc_start: 0.7721 (pt) cc_final: 0.7377 (pt) REVERT: E 90 MET cc_start: 0.8761 (mmm) cc_final: 0.8034 (tpp) REVERT: E 93 GLN cc_start: 0.8629 (tt0) cc_final: 0.7905 (tt0) REVERT: E 107 THR cc_start: 0.9235 (m) cc_final: 0.8930 (p) REVERT: E 109 LEU cc_start: 0.9056 (mp) cc_final: 0.8624 (mt) REVERT: E 112 ILE cc_start: 0.8880 (mm) cc_final: 0.8678 (mp) REVERT: E 113 HIS cc_start: 0.8933 (t70) cc_final: 0.7679 (t-90) REVERT: F 25 ASN cc_start: 0.8083 (m-40) cc_final: 0.7761 (m-40) REVERT: F 27 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8212 (mp10) REVERT: F 44 LYS cc_start: 0.8562 (mtpt) cc_final: 0.8068 (mtpp) REVERT: F 79 LYS cc_start: 0.7437 (mmtt) cc_final: 0.6677 (mmtt) REVERT: F 85 ASP cc_start: 0.8289 (m-30) cc_final: 0.8076 (m-30) REVERT: F 98 TYR cc_start: 0.9035 (m-10) cc_final: 0.8815 (m-10) REVERT: G 38 ASN cc_start: 0.8739 (m110) cc_final: 0.8185 (t0) REVERT: G 68 ASN cc_start: 0.9192 (m110) cc_final: 0.8914 (t0) REVERT: G 74 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8716 (mtmm) REVERT: G 95 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7977 (tmtt) REVERT: H 37 TYR cc_start: 0.8814 (m-80) cc_final: 0.7805 (m-80) REVERT: H 59 MET cc_start: 0.9206 (tpp) cc_final: 0.8741 (tpp) REVERT: H 68 ASP cc_start: 0.8637 (t0) cc_final: 0.8234 (t0) REVERT: H 95 GLN cc_start: 0.8997 (tt0) cc_final: 0.7953 (tm-30) REVERT: H 112 SER cc_start: 0.9080 (t) cc_final: 0.8735 (p) REVERT: H 113 GLU cc_start: 0.8311 (mp0) cc_final: 0.7942 (mp0) REVERT: K 78 PHE cc_start: 0.7736 (m-80) cc_final: 0.7455 (m-80) REVERT: K 103 LEU cc_start: 0.9286 (mt) cc_final: 0.8957 (mt) REVERT: K 107 THR cc_start: 0.9255 (p) cc_final: 0.8464 (p) REVERT: K 120 MET cc_start: 0.5400 (mtt) cc_final: 0.4650 (mtp) REVERT: K 123 ASP cc_start: 0.8654 (m-30) cc_final: 0.7699 (t0) REVERT: L 58 LEU cc_start: 0.9542 (mt) cc_final: 0.9261 (pp) REVERT: M 64 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8281 (tm-30) REVERT: M 84 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8512 (tm-30) REVERT: N 43 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8129 (tptp) REVERT: N 44 VAL cc_start: 0.9052 (t) cc_final: 0.8775 (t) REVERT: N 99 ARG cc_start: 0.8638 (ptm160) cc_final: 0.8289 (ptt90) REVERT: O 54 TYR cc_start: 0.8900 (m-80) cc_final: 0.8565 (m-10) REVERT: O 64 LYS cc_start: 0.8491 (pptt) cc_final: 0.8166 (pptt) REVERT: O 65 LEU cc_start: 0.8279 (tp) cc_final: 0.7855 (tp) REVERT: O 67 PHE cc_start: 0.8893 (t80) cc_final: 0.8411 (t80) REVERT: O 76 GLN cc_start: 0.9062 (tt0) cc_final: 0.8648 (tp40) REVERT: O 77 ASP cc_start: 0.8148 (m-30) cc_final: 0.7876 (m-30) REVERT: O 90 MET cc_start: 0.8825 (mtt) cc_final: 0.8592 (ptm) REVERT: O 96 CYS cc_start: 0.9498 (m) cc_final: 0.8556 (m) REVERT: O 101 VAL cc_start: 0.9432 (m) cc_final: 0.8908 (p) REVERT: O 105 GLU cc_start: 0.9269 (pt0) cc_final: 0.8954 (pt0) REVERT: P 44 LYS cc_start: 0.7208 (tttt) cc_final: 0.6960 (tptm) REVERT: P 59 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8764 (mmmm) outliers start: 2 outliers final: 1 residues processed: 392 average time/residue: 0.1499 time to fit residues: 90.7129 Evaluate side-chains 310 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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: 3.9990 chunk 75 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 133 optimal weight: 0.0000 chunk 83 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 95 GLN E 68 GLN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN M 31 HIS P 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.074112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.051426 restraints weight = 123736.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.052943 restraints weight = 60802.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.053907 restraints weight = 38888.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.054504 restraints weight = 29664.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.054854 restraints weight = 25373.385| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21551 Z= 0.213 Angle : 0.665 9.497 31255 Z= 0.386 Chirality : 0.037 0.207 3561 Planarity : 0.005 0.056 2220 Dihedral : 33.055 177.914 6852 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.10 % Allowed : 2.20 % Favored : 97.71 % 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 aren not related in a simple way. whole: 1.09 (0.23), residues: 1219 helix: 1.21 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.73 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 92 TYR 0.028 0.003 TYR E 99 PHE 0.028 0.002 PHE F 61 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00467 (21551) covalent geometry : angle 0.66483 (31255) hydrogen bonds : bond 0.05984 ( 1312) hydrogen bonds : angle 3.74257 ( 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 : 0.543 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: A 84 PHE cc_start: 0.8492 (m-80) cc_final: 0.8226 (m-80) REVERT: A 93 GLN cc_start: 0.9006 (tp40) cc_final: 0.8422 (tp40) REVERT: A 99 TYR cc_start: 0.8656 (t80) cc_final: 0.8416 (t80) REVERT: A 105 GLU cc_start: 0.7465 (pp20) cc_final: 0.7143 (pp20) REVERT: B 52 GLU cc_start: 0.8487 (mp0) cc_final: 0.8163 (mp0) REVERT: B 63 GLU cc_start: 0.8654 (tt0) cc_final: 0.8081 (tm-30) REVERT: B 68 ASP cc_start: 0.8837 (m-30) cc_final: 0.8636 (m-30) REVERT: B 74 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 84 MET cc_start: 0.8330 (tpt) cc_final: 0.7578 (tpp) REVERT: B 88 TYR cc_start: 0.8176 (m-80) cc_final: 0.7731 (m-80) REVERT: B 98 TYR cc_start: 0.8792 (m-10) cc_final: 0.8426 (m-80) REVERT: C 112 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7756 (mm-40) REVERT: D 42 TYR cc_start: 0.8618 (t80) cc_final: 0.8417 (t80) REVERT: D 44 VAL cc_start: 0.9509 (t) cc_final: 0.9259 (p) REVERT: D 68 ASP cc_start: 0.8464 (t70) cc_final: 0.8240 (t0) REVERT: E 54 TYR cc_start: 0.8581 (m-10) cc_final: 0.7754 (m-80) REVERT: E 81 ASP cc_start: 0.7316 (t0) cc_final: 0.6947 (t0) REVERT: E 82 LEU cc_start: 0.7825 (pt) cc_final: 0.7604 (pt) REVERT: E 93 GLN cc_start: 0.8760 (tt0) cc_final: 0.8432 (tt0) REVERT: E 109 LEU cc_start: 0.9078 (mp) cc_final: 0.8597 (mt) REVERT: E 120 MET cc_start: 0.6817 (mpp) cc_final: 0.6599 (mpp) REVERT: F 25 ASN cc_start: 0.8049 (m-40) cc_final: 0.7665 (m110) REVERT: F 44 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8166 (mtpp) REVERT: F 79 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6432 (mmtt) REVERT: F 88 TYR cc_start: 0.8553 (m-10) cc_final: 0.8083 (m-80) REVERT: G 38 ASN cc_start: 0.8883 (m110) cc_final: 0.8492 (t0) REVERT: G 68 ASN cc_start: 0.9156 (m110) cc_final: 0.8823 (t0) REVERT: G 74 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8695 (mtmm) REVERT: G 95 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7903 (tmtt) REVERT: H 37 TYR cc_start: 0.8759 (m-80) cc_final: 0.7878 (m-80) REVERT: H 59 MET cc_start: 0.9152 (tpp) cc_final: 0.8930 (tpp) REVERT: H 112 SER cc_start: 0.9025 (t) cc_final: 0.8585 (p) REVERT: K 78 PHE cc_start: 0.7663 (m-80) cc_final: 0.7375 (m-80) REVERT: K 90 MET cc_start: 0.8451 (mmp) cc_final: 0.8241 (mmp) REVERT: K 103 LEU cc_start: 0.9258 (mt) cc_final: 0.8930 (mt) REVERT: K 120 MET cc_start: 0.5566 (mtt) cc_final: 0.4442 (mtp) REVERT: K 125 GLN cc_start: 0.8914 (pm20) cc_final: 0.8651 (pm20) REVERT: K 131 ARG cc_start: 0.7583 (tpp80) cc_final: 0.7226 (tpp80) REVERT: M 61 GLU cc_start: 0.9192 (pt0) cc_final: 0.8932 (pt0) REVERT: M 64 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8243 (tm-30) REVERT: N 43 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8209 (tptp) REVERT: O 54 TYR cc_start: 0.8983 (m-80) cc_final: 0.8638 (m-10) REVERT: O 64 LYS cc_start: 0.8444 (pptt) cc_final: 0.8166 (pptt) REVERT: O 65 LEU cc_start: 0.8308 (tp) cc_final: 0.7867 (tp) REVERT: O 67 PHE cc_start: 0.8817 (t80) cc_final: 0.8444 (t80) REVERT: O 76 GLN cc_start: 0.8994 (tt0) cc_final: 0.8600 (tp40) REVERT: O 90 MET cc_start: 0.8809 (mtt) cc_final: 0.8603 (ptm) REVERT: O 96 CYS cc_start: 0.9305 (m) cc_final: 0.8962 (m) REVERT: O 101 VAL cc_start: 0.9473 (m) cc_final: 0.8880 (p) REVERT: O 105 GLU cc_start: 0.9268 (pt0) cc_final: 0.8967 (pt0) REVERT: O 125 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8686 (mm-40) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.1397 time to fit residues: 79.0132 Evaluate side-chains 295 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 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** L 27 GLN 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 = 0.3726 r_free = 0.3726 target = 0.073674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.051136 restraints weight = 122454.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.052606 restraints weight = 60869.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053546 restraints weight = 39139.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.054135 restraints weight = 29906.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054471 restraints weight = 25580.632| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 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 = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21551 Z= 0.212 Angle : 0.678 9.967 31255 Z= 0.391 Chirality : 0.038 0.183 3561 Planarity : 0.005 0.058 2220 Dihedral : 33.161 177.348 6852 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.23), residues: 1219 helix: 1.03 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.85 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 92 TYR 0.033 0.002 TYR N 83 PHE 0.028 0.002 PHE E 67 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00464 (21551) covalent geometry : angle 0.67766 (31255) hydrogen bonds : bond 0.05812 ( 1312) hydrogen bonds : angle 3.79726 ( 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 352 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8483 (m-80) cc_final: 0.8193 (m-80) REVERT: A 93 GLN cc_start: 0.8985 (tp40) cc_final: 0.8395 (tp40) REVERT: A 105 GLU cc_start: 0.7357 (pp20) cc_final: 0.7146 (pp20) REVERT: B 45 ARG cc_start: 0.8122 (tpt-90) cc_final: 0.6948 (tpt-90) REVERT: B 52 GLU cc_start: 0.8515 (mp0) cc_final: 0.8178 (mp0) REVERT: B 63 GLU cc_start: 0.8614 (tt0) cc_final: 0.7451 (tm-30) REVERT: B 74 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7899 (tm-30) REVERT: B 98 TYR cc_start: 0.8796 (m-10) cc_final: 0.8561 (m-10) REVERT: C 35 ARG cc_start: 0.8955 (mtt90) cc_final: 0.8625 (mmt180) REVERT: C 56 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8573 (mm-30) REVERT: D 44 VAL cc_start: 0.9516 (t) cc_final: 0.9236 (p) REVERT: D 62 MET cc_start: 0.8711 (mmm) cc_final: 0.8233 (mmp) REVERT: D 68 ASP cc_start: 0.8430 (t70) cc_final: 0.8216 (t0) REVERT: D 82 HIS cc_start: 0.8483 (t70) cc_final: 0.8114 (t70) REVERT: E 54 TYR cc_start: 0.8415 (m-10) cc_final: 0.7719 (m-80) REVERT: E 60 LEU cc_start: 0.8620 (mp) cc_final: 0.8103 (tp) REVERT: E 81 ASP cc_start: 0.7427 (t0) cc_final: 0.7126 (t0) REVERT: E 94 GLU cc_start: 0.8532 (tt0) cc_final: 0.8069 (tt0) REVERT: E 106 ASP cc_start: 0.8999 (m-30) cc_final: 0.8673 (m-30) REVERT: F 25 ASN cc_start: 0.8101 (m-40) cc_final: 0.7712 (m110) REVERT: F 39 ARG cc_start: 0.8813 (mpt-90) cc_final: 0.8527 (mmm-85) REVERT: F 44 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8398 (mtpt) REVERT: F 79 LYS cc_start: 0.7344 (mmtt) cc_final: 0.6517 (mmtt) REVERT: F 88 TYR cc_start: 0.8467 (m-10) cc_final: 0.8062 (m-80) REVERT: G 38 ASN cc_start: 0.8883 (m110) cc_final: 0.8486 (t0) REVERT: G 57 TYR cc_start: 0.8614 (t80) cc_final: 0.7947 (t80) REVERT: G 68 ASN cc_start: 0.9176 (m110) cc_final: 0.8701 (t0) REVERT: G 95 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7831 (tmtt) REVERT: H 37 TYR cc_start: 0.8763 (m-80) cc_final: 0.7796 (m-80) REVERT: H 59 MET cc_start: 0.9168 (tpp) cc_final: 0.8923 (tpp) REVERT: H 112 SER cc_start: 0.8942 (t) cc_final: 0.8705 (m) REVERT: H 113 GLU cc_start: 0.8468 (mp0) cc_final: 0.7867 (mp0) REVERT: K 78 PHE cc_start: 0.7739 (m-80) cc_final: 0.7425 (m-80) REVERT: K 103 LEU cc_start: 0.9250 (mt) cc_final: 0.8920 (mt) REVERT: K 120 MET cc_start: 0.5482 (mtt) cc_final: 0.4400 (mtp) REVERT: K 125 GLN cc_start: 0.8861 (pm20) cc_final: 0.8602 (pm20) REVERT: K 131 ARG cc_start: 0.7624 (tpp80) cc_final: 0.7255 (tpp80) REVERT: M 61 GLU cc_start: 0.9177 (pt0) cc_final: 0.8955 (pt0) REVERT: M 64 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8167 (tm-30) REVERT: M 84 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8352 (tm-30) REVERT: N 43 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8208 (tptp) REVERT: N 45 LEU cc_start: 0.8894 (tt) cc_final: 0.8624 (tt) REVERT: N 99 ARG cc_start: 0.8566 (ptm160) cc_final: 0.8193 (ptt90) REVERT: O 54 TYR cc_start: 0.8957 (m-80) cc_final: 0.8634 (m-10) REVERT: O 64 LYS cc_start: 0.8492 (pptt) cc_final: 0.8154 (pptt) REVERT: O 65 LEU cc_start: 0.8324 (tp) cc_final: 0.7863 (tp) REVERT: O 67 PHE cc_start: 0.8840 (t80) cc_final: 0.8433 (t80) REVERT: O 76 GLN cc_start: 0.8994 (tt0) cc_final: 0.8627 (tp40) REVERT: O 96 CYS cc_start: 0.9362 (m) cc_final: 0.9027 (m) REVERT: O 105 GLU cc_start: 0.9293 (pt0) cc_final: 0.9039 (pt0) REVERT: P 44 LYS cc_start: 0.7662 (tptt) cc_final: 0.7412 (tppt) REVERT: P 59 LYS cc_start: 0.9385 (tptm) cc_final: 0.9029 (tppp) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1446 time to fit residues: 79.6053 Evaluate side-chains 284 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 10.0000 chunk 101 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN D 95 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN O 125 GLN P 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.071240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049293 restraints weight = 125395.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050734 restraints weight = 63769.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.051367 restraints weight = 36355.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051456 restraints weight = 31981.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.051534 restraints weight = 29862.120| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 21551 Z= 0.293 Angle : 0.751 13.191 31255 Z= 0.433 Chirality : 0.041 0.241 3561 Planarity : 0.006 0.056 2220 Dihedral : 33.673 179.304 6852 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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 aren not related in a simple way. whole: 0.31 (0.22), residues: 1219 helix: 0.67 (0.16), residues: 934 sheet: None (None), residues: 0 loop : -1.11 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 92 TYR 0.074 0.003 TYR L 88 PHE 0.060 0.003 PHE E 67 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00640 (21551) covalent geometry : angle 0.75091 (31255) hydrogen bonds : bond 0.07797 ( 1312) hydrogen bonds : angle 4.26520 ( 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 334 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.560 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: A 59 GLU cc_start: 0.8727 (pm20) cc_final: 0.8520 (pm20) REVERT: A 93 GLN cc_start: 0.8990 (tp40) cc_final: 0.8405 (tp40) REVERT: B 49 LEU cc_start: 0.8735 (tt) cc_final: 0.8526 (tt) REVERT: B 52 GLU cc_start: 0.8688 (mp0) cc_final: 0.8327 (mp0) REVERT: B 63 GLU cc_start: 0.8668 (tt0) cc_final: 0.7867 (tt0) REVERT: B 67 ARG cc_start: 0.8915 (tpp80) cc_final: 0.8211 (tpp80) REVERT: B 68 ASP cc_start: 0.9050 (m-30) cc_final: 0.8825 (m-30) REVERT: B 74 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7983 (tm-30) REVERT: C 35 ARG cc_start: 0.8960 (mtt90) cc_final: 0.8397 (mmm160) REVERT: D 42 TYR cc_start: 0.8857 (t80) cc_final: 0.8596 (t80) REVERT: D 44 VAL cc_start: 0.9547 (t) cc_final: 0.9304 (p) REVERT: D 68 ASP cc_start: 0.8399 (t70) cc_final: 0.8164 (t0) REVERT: E 54 TYR cc_start: 0.8511 (m-10) cc_final: 0.7779 (m-80) REVERT: E 81 ASP cc_start: 0.7161 (t0) cc_final: 0.6814 (t0) REVERT: E 93 GLN cc_start: 0.8588 (tt0) cc_final: 0.8164 (tp40) REVERT: F 25 ASN cc_start: 0.8166 (m-40) cc_final: 0.7774 (m110) REVERT: F 27 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8085 (mp10) REVERT: F 44 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8561 (mtpt) REVERT: F 79 LYS cc_start: 0.7346 (mmtt) cc_final: 0.6562 (mmtt) REVERT: F 85 ASP cc_start: 0.8252 (m-30) cc_final: 0.7879 (m-30) REVERT: F 88 TYR cc_start: 0.8572 (m-10) cc_final: 0.8094 (m-80) REVERT: G 38 ASN cc_start: 0.9017 (m110) cc_final: 0.8492 (t0) REVERT: G 68 ASN cc_start: 0.9151 (m110) cc_final: 0.8661 (t0) REVERT: G 95 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7891 (tmtt) REVERT: H 37 TYR cc_start: 0.8775 (m-80) cc_final: 0.7892 (m-80) REVERT: H 112 SER cc_start: 0.9259 (t) cc_final: 0.8931 (m) REVERT: H 113 GLU cc_start: 0.8605 (mp0) cc_final: 0.8236 (mp0) REVERT: K 78 PHE cc_start: 0.7700 (m-80) cc_final: 0.7392 (m-80) REVERT: K 90 MET cc_start: 0.8766 (mmp) cc_final: 0.8445 (mmp) REVERT: K 103 LEU cc_start: 0.9169 (mt) cc_final: 0.8870 (mt) REVERT: K 120 MET cc_start: 0.5564 (mtt) cc_final: 0.4439 (mtp) REVERT: K 125 GLN cc_start: 0.8826 (pm20) cc_final: 0.8578 (pm20) REVERT: M 61 GLU cc_start: 0.9152 (pt0) cc_final: 0.8923 (pt0) REVERT: M 64 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8116 (tm-30) REVERT: M 68 ASN cc_start: 0.9097 (m110) cc_final: 0.8844 (m110) REVERT: N 43 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8302 (tptp) REVERT: O 54 TYR cc_start: 0.8943 (m-80) cc_final: 0.8520 (m-10) REVERT: O 64 LYS cc_start: 0.8524 (pptt) cc_final: 0.8218 (pptt) REVERT: O 65 LEU cc_start: 0.8354 (tp) cc_final: 0.7889 (tp) REVERT: O 67 PHE cc_start: 0.8838 (t80) cc_final: 0.8401 (t80) REVERT: O 76 GLN cc_start: 0.8836 (tt0) cc_final: 0.8628 (pt0) REVERT: O 84 PHE cc_start: 0.6680 (m-80) cc_final: 0.5489 (p90) REVERT: O 96 CYS cc_start: 0.9507 (m) cc_final: 0.9108 (m) REVERT: O 105 GLU cc_start: 0.9364 (pt0) cc_final: 0.9053 (pt0) REVERT: P 59 LYS cc_start: 0.9419 (tptm) cc_final: 0.9013 (tppp) REVERT: P 85 ASP cc_start: 0.6892 (m-30) cc_final: 0.6662 (m-30) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.1475 time to fit residues: 76.3312 Evaluate side-chains 273 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 10.0000 chunk 8 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 68 GLN E 113 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN P 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.071706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049971 restraints weight = 127649.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.051374 restraints weight = 66413.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052155 restraints weight = 37995.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052186 restraints weight = 32943.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.052236 restraints weight = 30251.189| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.7771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21551 Z= 0.269 Angle : 0.742 12.457 31255 Z= 0.426 Chirality : 0.040 0.216 3561 Planarity : 0.006 0.058 2220 Dihedral : 33.746 178.112 6852 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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 aren not related in a simple way. whole: 0.06 (0.22), residues: 1219 helix: 0.56 (0.16), residues: 933 sheet: None (None), residues: 0 loop : -1.44 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 42 TYR 0.056 0.003 TYR L 88 PHE 0.042 0.003 PHE F 61 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00589 (21551) covalent geometry : angle 0.74229 (31255) hydrogen bonds : bond 0.06979 ( 1312) hydrogen bonds : angle 4.20490 ( 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 327 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8964 (tp40) cc_final: 0.8383 (tp40) REVERT: A 120 MET cc_start: 0.8960 (mtm) cc_final: 0.8689 (mpp) REVERT: B 44 LYS cc_start: 0.7992 (tttm) cc_final: 0.7636 (tttt) REVERT: B 45 ARG cc_start: 0.8319 (tpt-90) cc_final: 0.7898 (tpt-90) REVERT: B 52 GLU cc_start: 0.8737 (mp0) cc_final: 0.8365 (mp0) REVERT: B 74 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7930 (tm-30) REVERT: C 35 ARG cc_start: 0.8918 (mtt90) cc_final: 0.8384 (mmm160) REVERT: D 44 VAL cc_start: 0.9563 (t) cc_final: 0.9307 (p) REVERT: D 62 MET cc_start: 0.8690 (mmm) cc_final: 0.8316 (mmp) REVERT: D 68 ASP cc_start: 0.8370 (t70) cc_final: 0.8087 (t0) REVERT: D 83 TYR cc_start: 0.8296 (t80) cc_final: 0.7170 (t80) REVERT: D 100 LEU cc_start: 0.8894 (mm) cc_final: 0.8558 (mm) REVERT: E 54 TYR cc_start: 0.8467 (m-10) cc_final: 0.7725 (m-80) REVERT: E 60 LEU cc_start: 0.9096 (mp) cc_final: 0.7660 (mp) REVERT: E 81 ASP cc_start: 0.7162 (t0) cc_final: 0.6869 (t0) REVERT: E 93 GLN cc_start: 0.8766 (tt0) cc_final: 0.7936 (tm-30) REVERT: E 94 GLU cc_start: 0.8602 (tt0) cc_final: 0.8012 (tt0) REVERT: E 97 GLU cc_start: 0.8786 (pm20) cc_final: 0.7778 (pm20) REVERT: F 25 ASN cc_start: 0.7995 (m-40) cc_final: 0.7555 (m110) REVERT: F 44 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8411 (mtpp) REVERT: F 79 LYS cc_start: 0.7345 (mmtt) cc_final: 0.7022 (tptt) REVERT: F 85 ASP cc_start: 0.8252 (m-30) cc_final: 0.8005 (m-30) REVERT: F 88 TYR cc_start: 0.8560 (m-10) cc_final: 0.8127 (m-80) REVERT: G 38 ASN cc_start: 0.8929 (m110) cc_final: 0.8470 (t0) REVERT: G 68 ASN cc_start: 0.9144 (m110) cc_final: 0.8640 (t0) REVERT: G 95 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7885 (tmtt) REVERT: H 37 TYR cc_start: 0.8687 (m-80) cc_final: 0.7897 (m-80) REVERT: H 112 SER cc_start: 0.9213 (t) cc_final: 0.8786 (m) REVERT: K 78 PHE cc_start: 0.7662 (m-80) cc_final: 0.7332 (m-80) REVERT: K 103 LEU cc_start: 0.9075 (mt) cc_final: 0.8868 (mt) REVERT: K 107 THR cc_start: 0.9143 (p) cc_final: 0.8420 (p) REVERT: K 120 MET cc_start: 0.5836 (mtt) cc_final: 0.5004 (mtp) REVERT: K 123 ASP cc_start: 0.8599 (m-30) cc_final: 0.8082 (t0) REVERT: K 131 ARG cc_start: 0.7555 (tpp80) cc_final: 0.7328 (tpp80) REVERT: M 61 GLU cc_start: 0.9144 (pt0) cc_final: 0.8871 (pt0) REVERT: M 64 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8133 (tm-30) REVERT: M 68 ASN cc_start: 0.9089 (m110) cc_final: 0.8805 (m110) REVERT: N 43 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8381 (tptp) REVERT: N 102 LEU cc_start: 0.7902 (mm) cc_final: 0.7673 (tp) REVERT: O 54 TYR cc_start: 0.8937 (m-80) cc_final: 0.8514 (m-10) REVERT: O 64 LYS cc_start: 0.8526 (pptt) cc_final: 0.8214 (pptt) REVERT: O 65 LEU cc_start: 0.8372 (tp) cc_final: 0.7901 (tp) REVERT: O 67 PHE cc_start: 0.8883 (t80) cc_final: 0.8414 (t80) REVERT: O 96 CYS cc_start: 0.9251 (m) cc_final: 0.8821 (m) REVERT: O 105 GLU cc_start: 0.9343 (pt0) cc_final: 0.9025 (pt0) REVERT: O 125 GLN cc_start: 0.9202 (mm110) cc_final: 0.8826 (mm-40) REVERT: P 59 LYS cc_start: 0.9449 (tptm) cc_final: 0.9066 (tppp) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1426 time to fit residues: 72.6612 Evaluate side-chains 269 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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: 10.0000 chunk 92 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.072298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049744 restraints weight = 125109.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050958 restraints weight = 66718.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051411 restraints weight = 39877.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.051559 restraints weight = 37504.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051604 restraints weight = 34162.487| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.8040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 21551 Z= 0.253 Angle : 0.734 11.752 31255 Z= 0.421 Chirality : 0.040 0.176 3561 Planarity : 0.006 0.074 2220 Dihedral : 33.770 179.011 6852 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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 aren not related in a simple way. whole: 0.08 (0.22), residues: 1219 helix: 0.58 (0.16), residues: 934 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 92 TYR 0.053 0.003 TYR L 88 PHE 0.042 0.003 PHE E 67 HIS 0.011 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00557 (21551) covalent geometry : angle 0.73359 (31255) hydrogen bonds : bond 0.06792 ( 1312) hydrogen bonds : angle 4.16897 ( 3284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3563.64 seconds wall clock time: 62 minutes 24.94 seconds (3744.94 seconds total)