Starting phenix.real_space_refine on Tue May 20 03:36:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3f_38880/05_2025/8y3f_38880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3f_38880/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3f_38880/05_2025/8y3f_38880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3f_38880/05_2025/8y3f_38880.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3f_38880/05_2025/8y3f_38880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3f_38880/05_2025/8y3f_38880.cif" } resolution = 4.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.15, per 1000 atoms: 0.50 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: 5.12 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 9.11 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: 7.93 Time building geometry restraints manager: 5.98 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: 0.240 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 48.990 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.016 0.003 HIS H 109 PHE 0.037 0.003 PHE N 65 TYR 0.055 0.003 TYR D 83 ARG 0.008 0.001 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.10958 ( 1312) hydrogen bonds : angle 4.51121 ( 3284) covalent geometry : bond 0.00414 (21551) covalent geometry : angle 0.74559 (31255) *********************** 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 : 1.625 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 61 LEU cc_start: 0.8725 (mt) cc_final: 0.8193 (mp) REVERT: A 84 PHE cc_start: 0.7753 (m-80) cc_final: 0.7514 (m-10) REVERT: A 89 VAL cc_start: 0.9378 (t) cc_final: 0.9157 (p) REVERT: A 92 LEU cc_start: 0.9424 (mt) cc_final: 0.8825 (mt) REVERT: A 93 GLN cc_start: 0.8689 (tt0) cc_final: 0.8275 (tp40) REVERT: A 108 ASN cc_start: 0.8749 (t0) cc_final: 0.8118 (t0) REVERT: B 90 LEU cc_start: 0.9103 (mt) cc_final: 0.8704 (mp) REVERT: B 96 THR cc_start: 0.8661 (p) cc_final: 0.8314 (t) REVERT: C 25 PHE cc_start: 0.8607 (m-80) cc_final: 0.8382 (m-10) REVERT: C 26 PRO cc_start: 0.8556 (Cg_endo) cc_final: 0.8271 (Cg_exo) REVERT: C 78 ILE cc_start: 0.8793 (mm) cc_final: 0.8560 (mm) REVERT: C 91 GLU cc_start: 0.8521 (pm20) cc_final: 0.8245 (pp20) REVERT: C 110 ASN cc_start: 0.8874 (t0) cc_final: 0.8343 (t0) REVERT: D 34 LYS cc_start: 0.7417 (tptp) cc_final: 0.7079 (tppt) REVERT: D 42 TYR cc_start: 0.7662 (t80) cc_final: 0.7350 (t80) REVERT: D 95 GLN cc_start: 0.7832 (tt0) cc_final: 0.7396 (tt0) REVERT: D 100 LEU cc_start: 0.9272 (mp) cc_final: 0.8712 (mm) REVERT: E 60 LEU cc_start: 0.9028 (mt) cc_final: 0.7836 (mp) REVERT: E 93 GLN cc_start: 0.9290 (tt0) cc_final: 0.8246 (tt0) REVERT: E 101 VAL cc_start: 0.9409 (m) cc_final: 0.9183 (p) REVERT: E 106 ASP cc_start: 0.8221 (m-30) cc_final: 0.7931 (m-30) REVERT: E 107 THR cc_start: 0.9172 (m) cc_final: 0.8614 (p) REVERT: F 25 ASN cc_start: 0.7342 (m-40) cc_final: 0.6892 (m-40) REVERT: F 49 LEU cc_start: 0.7418 (mp) cc_final: 0.6801 (mt) REVERT: F 59 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8351 (tttt) REVERT: F 85 ASP cc_start: 0.8698 (m-30) cc_final: 0.8112 (m-30) REVERT: H 37 TYR cc_start: 0.8047 (m-80) cc_final: 0.7638 (m-80) REVERT: H 42 TYR cc_start: 0.7127 (t80) cc_final: 0.6851 (t80) REVERT: H 45 LEU cc_start: 0.7677 (tp) cc_final: 0.7387 (tp) REVERT: H 57 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7817 (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: 0.8743 (mm) REVERT: H 65 PHE cc_start: 0.8710 (t80) cc_final: 0.8300 (t80) REVERT: H 68 ASP cc_start: 0.6642 (t0) cc_final: 0.5868 (t0) REVERT: H 71 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6796 (mt-10) REVERT: H 101 LEU cc_start: 0.8643 (mp) cc_final: 0.8359 (mt) REVERT: K 73 GLU cc_start: 0.6468 (tt0) cc_final: 0.5961 (tp30) REVERT: L 27 GLN cc_start: 0.7049 (mp10) cc_final: 0.6821 (tp-100) REVERT: L 30 THR cc_start: 0.7324 (p) cc_final: 0.6880 (t) REVERT: L 86 VAL cc_start: 0.4849 (t) cc_final: 0.4584 (t) REVERT: L 87 VAL cc_start: 0.7019 (t) cc_final: 0.6535 (p) REVERT: L 88 TYR cc_start: 0.2709 (m-10) cc_final: 0.2139 (m-10) REVERT: N 41 VAL cc_start: 0.8862 (t) cc_final: 0.8592 (t) REVERT: N 54 ILE cc_start: 0.6873 (tt) cc_final: 0.6554 (pt) REVERT: N 62 MET cc_start: 0.7795 (mmm) cc_final: 0.7364 (mmp) REVERT: N 68 ASP cc_start: 0.7005 (t70) cc_final: 0.6690 (t0) REVERT: O 61 LEU cc_start: 0.8036 (mt) cc_final: 0.7502 (mt) REVERT: O 74 ILE cc_start: 0.8047 (tp) cc_final: 0.7694 (mm) REVERT: O 76 GLN cc_start: 0.8229 (tt0) cc_final: 0.7895 (tp40) REVERT: O 92 LEU cc_start: 0.8472 (mm) cc_final: 0.8128 (mm) REVERT: O 103 LEU cc_start: 0.8743 (tp) cc_final: 0.8483 (tt) REVERT: P 93 GLN cc_start: 0.8772 (tt0) cc_final: 0.8442 (tm-30) outliers start: 0 outliers final: 0 residues processed: 592 average time/residue: 0.3900 time to fit residues: 325.0556 Evaluate side-chains 381 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 152 optimal weight: 40.0000 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** M 68 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** M 89 ASN N 109 HIS P 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.082437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.060794 restraints weight = 126157.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061633 restraints weight = 73967.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.061968 restraints weight = 48888.750| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 21551 Z= 0.276 Angle : 0.726 13.338 31255 Z= 0.419 Chirality : 0.040 0.193 3561 Planarity : 0.007 0.098 2220 Dihedral : 32.740 178.985 6852 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.22), residues: 1219 helix: 1.31 (0.16), residues: 928 sheet: None (None), residues: 0 loop : -0.22 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS M 82 PHE 0.017 0.003 PHE N 65 TYR 0.046 0.003 TYR B 88 ARG 0.008 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.07160 ( 1312) hydrogen bonds : angle 4.01028 ( 3284) covalent geometry : bond 0.00598 (21551) covalent geometry : angle 0.72607 (31255) *********************** 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 418 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 417 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9222 (mt) cc_final: 0.8992 (mm) REVERT: A 76 GLN cc_start: 0.8630 (tp40) cc_final: 0.8320 (tp40) REVERT: A 84 PHE cc_start: 0.8384 (m-80) cc_final: 0.8125 (m-80) REVERT: A 110 CYS cc_start: 0.9260 (m) cc_final: 0.9022 (m) REVERT: B 40 ARG cc_start: 0.9177 (mtp180) cc_final: 0.8958 (tpp80) REVERT: B 45 ARG cc_start: 0.7490 (mtp85) cc_final: 0.7238 (tpt-90) REVERT: B 59 LYS cc_start: 0.9049 (tptt) cc_final: 0.8512 (tptp) REVERT: B 63 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7667 (mt-10) REVERT: B 74 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 98 TYR cc_start: 0.8801 (m-10) cc_final: 0.8557 (m-10) REVERT: C 25 PHE cc_start: 0.8625 (m-80) cc_final: 0.7892 (m-10) REVERT: C 104 GLN cc_start: 0.8347 (mt0) cc_final: 0.7829 (mt0) REVERT: C 110 ASN cc_start: 0.9133 (t0) cc_final: 0.8707 (m110) REVERT: D 34 LYS cc_start: 0.7504 (tptp) cc_final: 0.7229 (tppt) REVERT: D 42 TYR cc_start: 0.8482 (t80) cc_final: 0.8279 (t80) REVERT: D 44 VAL cc_start: 0.9452 (t) cc_final: 0.9096 (p) REVERT: D 68 ASP cc_start: 0.8419 (t70) cc_final: 0.8130 (t0) REVERT: D 82 HIS cc_start: 0.8198 (t-90) cc_final: 0.7892 (t70) REVERT: D 95 GLN cc_start: 0.8522 (tt0) cc_final: 0.8199 (tt0) REVERT: E 46 VAL cc_start: 0.7900 (t) cc_final: 0.7661 (t) REVERT: E 54 TYR cc_start: 0.8344 (m-10) cc_final: 0.7529 (m-80) REVERT: E 93 GLN cc_start: 0.9149 (tt0) cc_final: 0.8497 (tm-30) REVERT: E 106 ASP cc_start: 0.8647 (m-30) cc_final: 0.8296 (m-30) REVERT: F 44 LYS cc_start: 0.8703 (ttpp) cc_final: 0.7886 (mtpt) REVERT: F 64 ASN cc_start: 0.8931 (m110) cc_final: 0.8647 (m110) REVERT: F 79 LYS cc_start: 0.7325 (mmtt) cc_final: 0.6741 (tptp) REVERT: F 88 TYR cc_start: 0.8650 (m-80) cc_final: 0.8155 (m-80) REVERT: G 35 ARG cc_start: 0.8202 (mtm180) cc_final: 0.7793 (ptp90) REVERT: G 38 ASN cc_start: 0.8323 (m110) cc_final: 0.8044 (m110) REVERT: H 68 ASP cc_start: 0.8640 (t0) cc_final: 0.8004 (t0) REVERT: H 94 ILE cc_start: 0.9510 (mm) cc_final: 0.9273 (mm) REVERT: H 106 LEU cc_start: 0.9568 (mt) cc_final: 0.9077 (mt) REVERT: H 112 SER cc_start: 0.9150 (t) cc_final: 0.8860 (p) REVERT: K 106 ASP cc_start: 0.9408 (m-30) cc_final: 0.9139 (m-30) REVERT: L 64 ASN cc_start: 0.9449 (t0) cc_final: 0.9189 (t0) REVERT: L 85 ASP cc_start: 0.5430 (m-30) cc_final: 0.5200 (m-30) REVERT: M 58 LEU cc_start: 0.8891 (mp) cc_final: 0.8633 (pp) REVERT: M 64 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8069 (tm-30) REVERT: M 84 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8623 (tm-30) REVERT: M 107 VAL cc_start: 0.8988 (t) cc_final: 0.8750 (p) REVERT: N 44 VAL cc_start: 0.9179 (t) cc_final: 0.8923 (t) REVERT: N 68 ASP cc_start: 0.8626 (t70) cc_final: 0.8130 (t0) REVERT: N 71 GLU cc_start: 0.8607 (pp20) cc_final: 0.8174 (pp20) REVERT: N 102 LEU cc_start: 0.8461 (mm) cc_final: 0.8249 (mm) REVERT: O 41 TYR cc_start: 0.6090 (m-80) cc_final: 0.5590 (m-80) REVERT: O 60 LEU cc_start: 0.5554 (mp) cc_final: 0.4910 (mp) REVERT: O 61 LEU cc_start: 0.8598 (mt) cc_final: 0.8107 (mp) REVERT: O 65 LEU cc_start: 0.7947 (tp) cc_final: 0.7642 (tp) REVERT: O 68 GLN cc_start: 0.9110 (mt0) cc_final: 0.8898 (mt0) REVERT: O 76 GLN cc_start: 0.9286 (tt0) cc_final: 0.8774 (tp40) REVERT: O 96 CYS cc_start: 0.9313 (m) cc_final: 0.9025 (m) REVERT: O 105 GLU cc_start: 0.9270 (pt0) cc_final: 0.8973 (pt0) REVERT: P 57 VAL cc_start: 0.9438 (t) cc_final: 0.9218 (p) REVERT: P 84 MET cc_start: 0.6724 (tpp) cc_final: 0.6521 (tpp) REVERT: P 88 TYR cc_start: 0.7554 (m-80) cc_final: 0.7172 (t80) REVERT: P 93 GLN cc_start: 0.8831 (tt0) cc_final: 0.8301 (tm-30) outliers start: 1 outliers final: 0 residues processed: 418 average time/residue: 0.3241 time to fit residues: 203.2287 Evaluate side-chains 311 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 110 ASN E 125 GLN ** F 25 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** M 68 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** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.074170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.052169 restraints weight = 118754.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.053630 restraints weight = 59552.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.054572 restraints weight = 37823.578| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21551 Z= 0.249 Angle : 0.686 10.246 31255 Z= 0.399 Chirality : 0.038 0.199 3561 Planarity : 0.006 0.071 2220 Dihedral : 33.030 179.270 6852 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.19 % Allowed : 5.35 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1219 helix: 1.27 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -0.39 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS M 82 PHE 0.019 0.002 PHE N 65 TYR 0.018 0.003 TYR M 57 ARG 0.010 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.06258 ( 1312) hydrogen bonds : angle 3.88649 ( 3284) covalent geometry : bond 0.00537 (21551) covalent geometry : angle 0.68622 (31255) *********************** 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 392 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 390 time to evaluate : 1.578 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: 0.8319 (m-80) cc_final: 0.7999 (m-10) REVERT: A 93 GLN cc_start: 0.9295 (tt0) cc_final: 0.8533 (tp40) REVERT: A 106 ASP cc_start: 0.9050 (m-30) cc_final: 0.8832 (m-30) REVERT: A 110 CYS cc_start: 0.9251 (m) cc_final: 0.8982 (m) REVERT: A 120 MET cc_start: 0.9198 (mtm) cc_final: 0.8955 (mtp) REVERT: B 40 ARG cc_start: 0.8941 (mtp180) cc_final: 0.8630 (tpp80) REVERT: B 52 GLU cc_start: 0.8675 (mp0) cc_final: 0.8268 (mp0) REVERT: B 74 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 88 TYR cc_start: 0.8057 (m-10) cc_final: 0.7171 (m-10) REVERT: B 98 TYR cc_start: 0.8879 (m-10) cc_final: 0.8486 (m-10) REVERT: C 39 TYR cc_start: 0.8945 (m-80) cc_final: 0.8285 (m-80) REVERT: D 42 TYR cc_start: 0.8636 (t80) cc_final: 0.8419 (t80) REVERT: D 44 VAL cc_start: 0.9478 (t) cc_final: 0.9130 (p) REVERT: D 62 MET cc_start: 0.8473 (mmm) cc_final: 0.8139 (mmp) REVERT: D 68 ASP cc_start: 0.8568 (t70) cc_final: 0.8315 (t0) REVERT: D 82 HIS cc_start: 0.8392 (t-90) cc_final: 0.8143 (t70) REVERT: D 89 ILE cc_start: 0.8855 (mt) cc_final: 0.8499 (tt) REVERT: D 100 LEU cc_start: 0.9202 (mm) cc_final: 0.8918 (mm) REVERT: D 108 LYS cc_start: 0.9244 (mttm) cc_final: 0.8958 (mtpt) REVERT: E 50 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7776 (tp30) REVERT: E 59 GLU cc_start: 0.7924 (pm20) cc_final: 0.7703 (pm20) REVERT: E 81 ASP cc_start: 0.7686 (t0) cc_final: 0.7365 (t0) REVERT: E 93 GLN cc_start: 0.9052 (tt0) cc_final: 0.8328 (tt0) REVERT: E 103 LEU cc_start: 0.9329 (tt) cc_final: 0.9044 (tt) REVERT: E 106 ASP cc_start: 0.8764 (m-30) cc_final: 0.8507 (m-30) REVERT: F 79 LYS cc_start: 0.7374 (mmtt) cc_final: 0.7018 (tptt) REVERT: F 88 TYR cc_start: 0.8551 (m-10) cc_final: 0.8194 (m-80) REVERT: G 35 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7582 (ptp90) REVERT: G 38 ASN cc_start: 0.8494 (m110) cc_final: 0.8243 (t0) REVERT: G 68 ASN cc_start: 0.9217 (m110) cc_final: 0.8869 (m-40) REVERT: G 95 LYS cc_start: 0.8380 (ttmt) cc_final: 0.7767 (tmtt) REVERT: H 37 TYR cc_start: 0.8936 (m-80) cc_final: 0.7765 (m-80) REVERT: H 54 ILE cc_start: 0.8712 (mp) cc_final: 0.8317 (mp) REVERT: H 68 ASP cc_start: 0.8880 (t0) cc_final: 0.8570 (t0) REVERT: H 112 SER cc_start: 0.9188 (t) cc_final: 0.8876 (p) REVERT: K 120 MET cc_start: 0.5285 (mtt) cc_final: 0.4985 (mtp) REVERT: M 84 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8518 (tm-30) REVERT: N 102 LEU cc_start: 0.8182 (mm) cc_final: 0.7951 (mm) REVERT: O 53 ARG cc_start: 0.9269 (tpp-160) cc_final: 0.8792 (ptm160) REVERT: O 54 TYR cc_start: 0.8965 (m-80) cc_final: 0.8116 (m-80) REVERT: O 61 LEU cc_start: 0.8050 (mt) cc_final: 0.7729 (mp) REVERT: O 64 LYS cc_start: 0.8509 (pptt) cc_final: 0.8195 (pptt) REVERT: O 65 LEU cc_start: 0.8158 (tp) cc_final: 0.7719 (tp) REVERT: O 68 GLN cc_start: 0.9090 (mt0) cc_final: 0.8785 (mt0) REVERT: O 76 GLN cc_start: 0.9056 (tt0) cc_final: 0.8542 (tp40) REVERT: O 92 LEU cc_start: 0.9099 (mm) cc_final: 0.8829 (mm) REVERT: O 96 CYS cc_start: 0.9545 (m) cc_final: 0.9340 (m) REVERT: O 99 TYR cc_start: 0.8331 (t80) cc_final: 0.7798 (t80) REVERT: O 101 VAL cc_start: 0.9465 (m) cc_final: 0.8928 (p) REVERT: O 105 GLU cc_start: 0.9255 (pt0) cc_final: 0.9000 (pt0) REVERT: P 44 LYS cc_start: 0.7495 (tttt) cc_final: 0.7177 (ttmm) REVERT: P 57 VAL cc_start: 0.9345 (t) cc_final: 0.9131 (p) REVERT: P 61 PHE cc_start: 0.9030 (t80) cc_final: 0.8562 (t80) REVERT: P 84 MET cc_start: 0.7364 (tpp) cc_final: 0.7037 (tpp) REVERT: P 88 TYR cc_start: 0.8216 (m-80) cc_final: 0.6792 (t80) REVERT: P 93 GLN cc_start: 0.8532 (tt0) cc_final: 0.8118 (tm-30) outliers start: 2 outliers final: 0 residues processed: 392 average time/residue: 0.3126 time to fit residues: 185.6870 Evaluate side-chains 306 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 147 optimal weight: 40.0000 chunk 154 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN M 68 ASN ** M 84 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 = 0.3769 r_free = 0.3769 target = 0.076286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054507 restraints weight = 117559.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056061 restraints weight = 56931.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057050 restraints weight = 35542.212| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21551 Z= 0.158 Angle : 0.616 7.686 31255 Z= 0.361 Chirality : 0.036 0.164 3561 Planarity : 0.005 0.069 2220 Dihedral : 32.717 179.266 6852 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1219 helix: 1.46 (0.16), residues: 933 sheet: None (None), residues: 0 loop : -0.35 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 82 PHE 0.020 0.002 PHE N 65 TYR 0.030 0.002 TYR C 57 ARG 0.009 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 1312) hydrogen bonds : angle 3.47375 ( 3284) covalent geometry : bond 0.00341 (21551) covalent geometry : angle 0.61584 (31255) *********************** 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 405 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.371 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: A 57 SER cc_start: 0.9007 (t) cc_final: 0.7897 (p) REVERT: A 62 ILE cc_start: 0.9008 (mt) cc_final: 0.8359 (mm) REVERT: A 84 PHE cc_start: 0.8136 (m-80) cc_final: 0.7846 (m-10) REVERT: A 110 CYS cc_start: 0.9273 (m) cc_final: 0.8802 (t) REVERT: A 123 ASP cc_start: 0.8203 (m-30) cc_final: 0.7641 (m-30) REVERT: B 37 LEU cc_start: 0.9390 (mm) cc_final: 0.9112 (mm) REVERT: B 40 ARG cc_start: 0.8868 (mtp180) cc_final: 0.8480 (tpp80) REVERT: B 63 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 67 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8407 (ttm110) REVERT: B 68 ASP cc_start: 0.9132 (m-30) cc_final: 0.8719 (m-30) REVERT: B 74 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 79 LYS cc_start: 0.7766 (mtmm) cc_final: 0.7123 (tttm) REVERT: B 84 MET cc_start: 0.7421 (tpp) cc_final: 0.7178 (tpp) REVERT: B 88 TYR cc_start: 0.7858 (m-10) cc_final: 0.5987 (m-10) REVERT: B 98 TYR cc_start: 0.8871 (m-10) cc_final: 0.8276 (m-10) REVERT: C 39 TYR cc_start: 0.8986 (m-80) cc_final: 0.8261 (m-80) REVERT: C 104 GLN cc_start: 0.8657 (mt0) cc_final: 0.7783 (mm-40) REVERT: C 110 ASN cc_start: 0.8860 (t0) cc_final: 0.8571 (m110) REVERT: C 112 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7855 (mm-40) REVERT: D 44 VAL cc_start: 0.9366 (t) cc_final: 0.9006 (p) REVERT: D 68 ASP cc_start: 0.8528 (t70) cc_final: 0.8269 (t0) REVERT: D 96 THR cc_start: 0.9240 (t) cc_final: 0.8879 (p) REVERT: D 100 LEU cc_start: 0.9202 (mm) cc_final: 0.8867 (mm) REVERT: D 108 LYS cc_start: 0.9220 (mttm) cc_final: 0.8991 (mtmt) REVERT: E 50 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7789 (tp30) REVERT: E 67 PHE cc_start: 0.8121 (t80) cc_final: 0.7900 (t80) REVERT: E 107 THR cc_start: 0.9210 (m) cc_final: 0.8994 (m) REVERT: E 109 LEU cc_start: 0.9066 (mp) cc_final: 0.8486 (mt) REVERT: F 44 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8086 (mtpp) REVERT: G 35 ARG cc_start: 0.8254 (mtm180) cc_final: 0.7781 (mtm110) REVERT: G 38 ASN cc_start: 0.8266 (m110) cc_final: 0.7982 (t0) REVERT: G 68 ASN cc_start: 0.9112 (m110) cc_final: 0.8831 (t0) REVERT: G 95 LYS cc_start: 0.8280 (ttmt) cc_final: 0.8003 (tmtt) REVERT: G 101 THR cc_start: 0.8973 (t) cc_final: 0.8573 (p) REVERT: H 37 TYR cc_start: 0.8858 (m-80) cc_final: 0.7888 (m-10) REVERT: H 54 ILE cc_start: 0.8204 (mp) cc_final: 0.7830 (mp) REVERT: H 68 ASP cc_start: 0.8746 (t0) cc_final: 0.7913 (t0) REVERT: H 112 SER cc_start: 0.9113 (t) cc_final: 0.8738 (p) REVERT: K 120 MET cc_start: 0.5745 (mtt) cc_final: 0.5036 (mtp) REVERT: K 123 ASP cc_start: 0.8373 (m-30) cc_final: 0.8045 (m-30) REVERT: M 25 PHE cc_start: 0.7746 (m-10) cc_final: 0.7097 (m-10) REVERT: M 49 VAL cc_start: 0.8046 (t) cc_final: 0.7703 (p) REVERT: M 56 GLU cc_start: 0.8312 (tt0) cc_final: 0.7153 (tt0) REVERT: M 64 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8180 (tm-30) REVERT: O 41 TYR cc_start: 0.6316 (m-80) cc_final: 0.5416 (m-10) REVERT: O 61 LEU cc_start: 0.8697 (mt) cc_final: 0.7507 (mp) REVERT: O 64 LYS cc_start: 0.8511 (pptt) cc_final: 0.8209 (pptt) REVERT: O 65 LEU cc_start: 0.8185 (tp) cc_final: 0.7762 (tp) REVERT: O 76 GLN cc_start: 0.9069 (tt0) cc_final: 0.8544 (tp40) REVERT: O 96 CYS cc_start: 0.9471 (m) cc_final: 0.9265 (m) REVERT: O 97 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8679 (mp0) REVERT: O 101 VAL cc_start: 0.9410 (m) cc_final: 0.8904 (p) REVERT: O 105 GLU cc_start: 0.9257 (pt0) cc_final: 0.8962 (pt0) REVERT: P 84 MET cc_start: 0.7357 (tpp) cc_final: 0.7093 (tpp) REVERT: P 88 TYR cc_start: 0.8154 (m-80) cc_final: 0.6885 (t80) REVERT: P 95 ARG cc_start: 0.7903 (mmt90) cc_final: 0.7571 (mmm160) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.3231 time to fit residues: 200.9307 Evaluate side-chains 320 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 139 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 E 125 GLN F 25 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.077383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.054921 restraints weight = 120860.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.056408 restraints weight = 60712.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.057380 restraints weight = 38932.012| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21551 Z= 0.156 Angle : 0.609 7.779 31255 Z= 0.359 Chirality : 0.035 0.236 3561 Planarity : 0.005 0.050 2220 Dihedral : 32.586 179.867 6852 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1219 helix: 1.46 (0.16), residues: 934 sheet: None (None), residues: 0 loop : -0.35 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.020 0.002 PHE N 65 TYR 0.035 0.002 TYR L 88 ARG 0.007 0.001 ARG L 92 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 1312) hydrogen bonds : angle 3.42580 ( 3284) covalent geometry : bond 0.00337 (21551) covalent geometry : angle 0.60930 (31255) *********************** 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 398 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 1.354 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: 0.9104 (tp40) cc_final: 0.8207 (tp40) REVERT: A 106 ASP cc_start: 0.8938 (m-30) cc_final: 0.8336 (m-30) REVERT: A 110 CYS cc_start: 0.9233 (m) cc_final: 0.8597 (t) REVERT: A 120 MET cc_start: 0.9039 (mtp) cc_final: 0.8785 (mtp) REVERT: A 123 ASP cc_start: 0.8114 (m-30) cc_final: 0.7306 (t70) REVERT: B 37 LEU cc_start: 0.9497 (mm) cc_final: 0.9262 (mm) REVERT: B 40 ARG cc_start: 0.9013 (mtp180) cc_final: 0.8578 (tpp80) REVERT: B 45 ARG cc_start: 0.7757 (tpt-90) cc_final: 0.7338 (tpt-90) REVERT: B 63 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8353 (tm-30) REVERT: B 68 ASP cc_start: 0.9090 (m-30) cc_final: 0.8581 (m-30) REVERT: B 74 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 79 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7525 (mttp) REVERT: B 98 TYR cc_start: 0.8865 (m-10) cc_final: 0.8342 (m-10) REVERT: C 39 TYR cc_start: 0.8949 (m-80) cc_final: 0.8241 (m-80) REVERT: C 104 GLN cc_start: 0.8450 (mt0) cc_final: 0.7943 (mt0) REVERT: C 110 ASN cc_start: 0.8936 (t0) cc_final: 0.8565 (m110) REVERT: C 111 ILE cc_start: 0.9088 (mt) cc_final: 0.8877 (mm) REVERT: D 44 VAL cc_start: 0.9387 (t) cc_final: 0.8991 (p) REVERT: D 62 MET cc_start: 0.8723 (mmm) cc_final: 0.8444 (mmp) REVERT: D 89 ILE cc_start: 0.8983 (tt) cc_final: 0.8757 (mt) REVERT: D 100 LEU cc_start: 0.9152 (mm) cc_final: 0.8918 (mm) REVERT: E 50 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7792 (tp30) REVERT: E 62 ILE cc_start: 0.7924 (pt) cc_final: 0.7017 (pt) REVERT: E 67 PHE cc_start: 0.8186 (t80) cc_final: 0.7814 (t80) REVERT: E 82 LEU cc_start: 0.7688 (pt) cc_final: 0.7442 (pt) REVERT: E 92 LEU cc_start: 0.9320 (mt) cc_final: 0.9066 (mt) REVERT: E 93 GLN cc_start: 0.9091 (tt0) cc_final: 0.7179 (tp40) REVERT: E 94 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8532 (mt-10) REVERT: E 107 THR cc_start: 0.9231 (m) cc_final: 0.8953 (p) REVERT: E 109 LEU cc_start: 0.8958 (mp) cc_final: 0.8686 (mt) REVERT: F 44 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8124 (mtpt) REVERT: F 79 LYS cc_start: 0.7297 (mmtt) cc_final: 0.6596 (mmtt) REVERT: F 85 ASP cc_start: 0.8274 (m-30) cc_final: 0.8036 (m-30) REVERT: F 92 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8559 (ttp80) REVERT: G 35 ARG cc_start: 0.8369 (mtm180) cc_final: 0.7791 (mtm110) REVERT: G 38 ASN cc_start: 0.8293 (m110) cc_final: 0.8011 (t0) REVERT: G 68 ASN cc_start: 0.9175 (m110) cc_final: 0.8900 (m-40) REVERT: G 95 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7975 (tmtt) REVERT: H 37 TYR cc_start: 0.8784 (m-80) cc_final: 0.7909 (m-10) REVERT: H 61 ILE cc_start: 0.9003 (mm) cc_final: 0.8523 (mt) REVERT: H 68 ASP cc_start: 0.8549 (t0) cc_final: 0.7524 (t0) REVERT: H 112 SER cc_start: 0.9046 (t) cc_final: 0.8761 (p) REVERT: K 94 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7985 (mm-30) REVERT: K 103 LEU cc_start: 0.9283 (mt) cc_final: 0.8996 (mt) REVERT: K 120 MET cc_start: 0.5688 (mtt) cc_final: 0.4710 (mtp) REVERT: M 25 PHE cc_start: 0.7597 (m-10) cc_final: 0.7232 (m-10) REVERT: M 49 VAL cc_start: 0.7658 (t) cc_final: 0.7377 (p) REVERT: M 56 GLU cc_start: 0.7892 (tt0) cc_final: 0.7323 (tt0) REVERT: M 64 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8227 (tm-30) REVERT: O 41 TYR cc_start: 0.6467 (m-80) cc_final: 0.5909 (m-80) REVERT: O 54 TYR cc_start: 0.8959 (m-80) cc_final: 0.8624 (m-10) REVERT: O 61 LEU cc_start: 0.8643 (mt) cc_final: 0.6994 (mp) REVERT: O 64 LYS cc_start: 0.8495 (pptt) cc_final: 0.8226 (pptt) REVERT: O 65 LEU cc_start: 0.8177 (tp) cc_final: 0.7892 (tp) REVERT: O 76 GLN cc_start: 0.9068 (tt0) cc_final: 0.8656 (tp40) REVERT: O 90 MET cc_start: 0.9124 (ptp) cc_final: 0.8892 (ptm) REVERT: O 96 CYS cc_start: 0.9399 (m) cc_final: 0.8422 (m) REVERT: O 101 VAL cc_start: 0.9452 (m) cc_final: 0.8888 (p) REVERT: O 105 GLU cc_start: 0.9295 (pt0) cc_final: 0.8959 (pt0) REVERT: O 124 ILE cc_start: 0.9308 (mp) cc_final: 0.9016 (mp) REVERT: P 44 LYS cc_start: 0.6934 (tttt) cc_final: 0.6613 (tptm) REVERT: P 53 GLU cc_start: 0.8361 (tt0) cc_final: 0.7529 (tt0) REVERT: P 59 LYS cc_start: 0.9277 (mmmm) cc_final: 0.9033 (mmmm) REVERT: P 61 PHE cc_start: 0.8822 (t80) cc_final: 0.8456 (t80) REVERT: P 84 MET cc_start: 0.7149 (tpp) cc_final: 0.6840 (tpp) REVERT: P 88 TYR cc_start: 0.8171 (m-80) cc_final: 0.6902 (t80) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.3027 time to fit residues: 184.0080 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 : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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** C 24 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN O 125 GLN P 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.074539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052882 restraints weight = 117509.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.054421 restraints weight = 56613.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055395 restraints weight = 35338.159| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21551 Z= 0.202 Angle : 0.648 11.339 31255 Z= 0.378 Chirality : 0.036 0.160 3561 Planarity : 0.005 0.051 2220 Dihedral : 32.873 179.267 6852 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.23), residues: 1219 helix: 1.34 (0.16), residues: 934 sheet: None (None), residues: 0 loop : -0.51 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS B 75 PHE 0.018 0.002 PHE D 65 TYR 0.025 0.002 TYR L 88 ARG 0.005 0.001 ARG L 92 Details of bonding type rmsd hydrogen bonds : bond 0.05712 ( 1312) hydrogen bonds : angle 3.65303 ( 3284) covalent geometry : bond 0.00444 (21551) covalent geometry : angle 0.64770 (31255) *********************** 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 361 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 1.557 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: 0.8922 (tp40) cc_final: 0.8168 (tp40) REVERT: A 106 ASP cc_start: 0.9092 (m-30) cc_final: 0.8483 (m-30) REVERT: A 110 CYS cc_start: 0.9210 (m) cc_final: 0.8935 (t) REVERT: B 37 LEU cc_start: 0.9412 (mm) cc_final: 0.9180 (mm) REVERT: B 44 LYS cc_start: 0.7830 (tttm) cc_final: 0.7503 (tttt) REVERT: B 45 ARG cc_start: 0.7925 (tpt-90) cc_final: 0.6777 (tpt-90) REVERT: B 52 GLU cc_start: 0.8352 (mp0) cc_final: 0.8103 (mp0) REVERT: B 63 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 68 ASP cc_start: 0.8975 (m-30) cc_final: 0.8651 (m-30) REVERT: B 74 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 84 MET cc_start: 0.8348 (mmm) cc_final: 0.8011 (tpp) REVERT: B 98 TYR cc_start: 0.8868 (m-10) cc_final: 0.8045 (m-80) REVERT: C 39 TYR cc_start: 0.8829 (m-80) cc_final: 0.8170 (m-80) REVERT: C 104 GLN cc_start: 0.8466 (mt0) cc_final: 0.7737 (mm-40) REVERT: C 110 ASN cc_start: 0.9028 (t0) cc_final: 0.8567 (m110) REVERT: C 112 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7770 (mm-40) REVERT: D 44 VAL cc_start: 0.9461 (t) cc_final: 0.9153 (p) REVERT: E 50 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7063 (tp30) REVERT: E 54 TYR cc_start: 0.8500 (m-10) cc_final: 0.7263 (m-80) REVERT: E 62 ILE cc_start: 0.7787 (pt) cc_final: 0.7420 (pt) REVERT: E 82 LEU cc_start: 0.7886 (pt) cc_final: 0.7567 (pt) REVERT: E 92 LEU cc_start: 0.9312 (mt) cc_final: 0.9070 (mt) REVERT: E 93 GLN cc_start: 0.8930 (tt0) cc_final: 0.8032 (tp40) REVERT: E 94 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8601 (mt-10) REVERT: E 96 CYS cc_start: 0.7862 (m) cc_final: 0.7547 (m) REVERT: E 107 THR cc_start: 0.9207 (m) cc_final: 0.8917 (p) REVERT: E 109 LEU cc_start: 0.9050 (mp) cc_final: 0.8826 (mt) REVERT: E 113 HIS cc_start: 0.8480 (t70) cc_final: 0.8045 (t-90) REVERT: F 27 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8246 (mp10) REVERT: F 44 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8084 (mtpp) REVERT: F 79 LYS cc_start: 0.7287 (mmtt) cc_final: 0.6512 (mmtt) REVERT: F 88 TYR cc_start: 0.8716 (m-10) cc_final: 0.8479 (m-80) REVERT: G 38 ASN cc_start: 0.8492 (m110) cc_final: 0.8256 (t0) REVERT: G 61 GLU cc_start: 0.8641 (tp30) cc_final: 0.8206 (mm-30) REVERT: G 68 ASN cc_start: 0.9098 (m110) cc_final: 0.8808 (m-40) REVERT: G 95 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7968 (tmtt) REVERT: H 37 TYR cc_start: 0.8862 (m-80) cc_final: 0.7947 (m-10) REVERT: H 68 ASP cc_start: 0.8862 (t0) cc_final: 0.8071 (t0) REVERT: H 112 SER cc_start: 0.9318 (t) cc_final: 0.8962 (p) REVERT: K 107 THR cc_start: 0.9250 (p) cc_final: 0.8493 (p) REVERT: K 120 MET cc_start: 0.5322 (mtt) cc_final: 0.4652 (mtp) REVERT: K 123 ASP cc_start: 0.8749 (m-30) cc_final: 0.7825 (t0) REVERT: M 49 VAL cc_start: 0.7993 (t) cc_final: 0.7665 (p) REVERT: M 64 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8221 (tm-30) REVERT: M 115 LEU cc_start: 0.6948 (tp) cc_final: 0.6738 (tp) REVERT: N 43 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8111 (tptp) REVERT: N 44 VAL cc_start: 0.9011 (t) cc_final: 0.8784 (t) REVERT: N 54 ILE cc_start: 0.7494 (tt) cc_final: 0.7058 (tt) REVERT: N 111 VAL cc_start: 0.8646 (t) cc_final: 0.8400 (p) REVERT: O 41 TYR cc_start: 0.6551 (m-80) cc_final: 0.5946 (m-80) REVERT: O 54 TYR cc_start: 0.8997 (m-80) cc_final: 0.8744 (m-10) REVERT: O 65 LEU cc_start: 0.7999 (tp) cc_final: 0.7758 (tp) REVERT: O 76 GLN cc_start: 0.9023 (tt0) cc_final: 0.8495 (tp40) REVERT: O 96 CYS cc_start: 0.9464 (m) cc_final: 0.8511 (m) REVERT: O 101 VAL cc_start: 0.9488 (m) cc_final: 0.8950 (p) REVERT: O 105 GLU cc_start: 0.9263 (pt0) cc_final: 0.8956 (pt0) REVERT: P 59 LYS cc_start: 0.9355 (mmmm) cc_final: 0.9088 (mmmm) REVERT: P 72 TYR cc_start: 0.7476 (m-10) cc_final: 0.7224 (m-10) REVERT: P 84 MET cc_start: 0.7356 (tpp) cc_final: 0.7087 (tpp) outliers start: 2 outliers final: 1 residues processed: 360 average time/residue: 0.2915 time to fit residues: 163.6119 Evaluate side-chains 304 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 21 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 128 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** D 47 GLN D 95 GLN E 113 HIS G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.076573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.054203 restraints weight = 121578.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055726 restraints weight = 61087.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056672 restraints weight = 39074.119| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21551 Z= 0.161 Angle : 0.630 7.623 31255 Z= 0.366 Chirality : 0.036 0.179 3561 Planarity : 0.005 0.086 2220 Dihedral : 32.676 177.603 6852 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.10 % Allowed : 1.53 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1219 helix: 1.44 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -0.47 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 75 PHE 0.018 0.002 PHE F 61 TYR 0.045 0.002 TYR L 88 ARG 0.020 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 1312) hydrogen bonds : angle 3.46972 ( 3284) covalent geometry : bond 0.00348 (21551) covalent geometry : angle 0.63044 (31255) *********************** 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 366 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 1.328 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: 0.8855 (tp40) cc_final: 0.8321 (tp40) REVERT: A 99 TYR cc_start: 0.8686 (t80) cc_final: 0.8481 (t80) REVERT: A 106 ASP cc_start: 0.9014 (m-30) cc_final: 0.8404 (m-30) REVERT: A 110 CYS cc_start: 0.9223 (m) cc_final: 0.8850 (t) REVERT: B 37 LEU cc_start: 0.9454 (mm) cc_final: 0.9226 (mm) REVERT: B 45 ARG cc_start: 0.8141 (tpt-90) cc_final: 0.6909 (tpt-90) REVERT: B 68 ASP cc_start: 0.8933 (m-30) cc_final: 0.8720 (m-30) REVERT: B 74 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7720 (tm-30) REVERT: B 84 MET cc_start: 0.7924 (mmm) cc_final: 0.7191 (mmm) REVERT: B 98 TYR cc_start: 0.8946 (m-10) cc_final: 0.8372 (m-10) REVERT: C 39 TYR cc_start: 0.8800 (m-80) cc_final: 0.8053 (m-80) REVERT: C 104 GLN cc_start: 0.8331 (mt0) cc_final: 0.7792 (mt0) REVERT: C 110 ASN cc_start: 0.8952 (t0) cc_final: 0.8580 (m110) REVERT: C 112 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7761 (mm-40) REVERT: D 44 VAL cc_start: 0.9449 (t) cc_final: 0.9066 (p) REVERT: D 62 MET cc_start: 0.8633 (mmm) cc_final: 0.8325 (mmp) REVERT: D 68 ASP cc_start: 0.8409 (t70) cc_final: 0.8131 (t0) REVERT: D 100 LEU cc_start: 0.8909 (mm) cc_final: 0.8682 (mm) REVERT: E 50 GLU cc_start: 0.8329 (mm-30) cc_final: 0.6704 (tp30) REVERT: E 54 TYR cc_start: 0.8371 (m-10) cc_final: 0.7122 (m-80) REVERT: E 62 ILE cc_start: 0.8590 (pt) cc_final: 0.7292 (pt) REVERT: E 67 PHE cc_start: 0.8065 (t80) cc_final: 0.7691 (t80) REVERT: E 82 LEU cc_start: 0.7946 (pt) cc_final: 0.7703 (pt) REVERT: E 92 LEU cc_start: 0.9365 (mt) cc_final: 0.9158 (mt) REVERT: E 93 GLN cc_start: 0.9166 (tt0) cc_final: 0.7609 (tp40) REVERT: E 94 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8186 (mt-10) REVERT: E 107 THR cc_start: 0.9320 (m) cc_final: 0.8994 (p) REVERT: F 27 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8260 (mp10) REVERT: F 44 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8039 (mtpp) REVERT: F 79 LYS cc_start: 0.7418 (mmtt) cc_final: 0.6746 (mmtt) REVERT: F 98 TYR cc_start: 0.9023 (m-10) cc_final: 0.8784 (m-10) REVERT: G 38 ASN cc_start: 0.8654 (m110) cc_final: 0.8219 (t0) REVERT: G 68 ASN cc_start: 0.9179 (m110) cc_final: 0.8863 (m-40) REVERT: G 95 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7974 (tmtt) REVERT: H 37 TYR cc_start: 0.8722 (m-80) cc_final: 0.7806 (m-10) REVERT: H 61 ILE cc_start: 0.8913 (mm) cc_final: 0.8333 (mt) REVERT: H 68 ASP cc_start: 0.8354 (t0) cc_final: 0.7785 (t0) REVERT: H 95 GLN cc_start: 0.8950 (tt0) cc_final: 0.7836 (tm-30) REVERT: H 112 SER cc_start: 0.8907 (t) cc_final: 0.8591 (m) REVERT: K 65 LEU cc_start: 0.7420 (tp) cc_final: 0.7179 (tt) REVERT: K 90 MET cc_start: 0.8601 (mmp) cc_final: 0.8343 (mmp) REVERT: K 103 LEU cc_start: 0.9268 (mt) cc_final: 0.8973 (mt) REVERT: K 120 MET cc_start: 0.5470 (mtt) cc_final: 0.4463 (mtp) REVERT: L 62 LEU cc_start: 0.9700 (mm) cc_final: 0.9415 (mm) REVERT: L 88 TYR cc_start: 0.5095 (m-80) cc_final: 0.4766 (m-10) REVERT: M 25 PHE cc_start: 0.6160 (m-10) cc_final: 0.5798 (m-10) REVERT: M 49 VAL cc_start: 0.7858 (t) cc_final: 0.7543 (p) REVERT: M 68 ASN cc_start: 0.9206 (m110) cc_final: 0.8918 (t0) REVERT: M 72 ASP cc_start: 0.7842 (m-30) cc_final: 0.7349 (m-30) REVERT: M 115 LEU cc_start: 0.6935 (tp) cc_final: 0.6719 (tp) REVERT: N 43 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8091 (tptp) REVERT: N 45 LEU cc_start: 0.9088 (tt) cc_final: 0.8860 (tt) REVERT: O 41 TYR cc_start: 0.6800 (m-80) cc_final: 0.6178 (m-80) REVERT: O 45 THR cc_start: 0.6647 (p) cc_final: 0.6439 (p) REVERT: O 54 TYR cc_start: 0.8974 (m-80) cc_final: 0.8725 (m-10) REVERT: O 76 GLN cc_start: 0.9037 (tt0) cc_final: 0.8539 (tp40) REVERT: O 96 CYS cc_start: 0.9437 (m) cc_final: 0.8490 (m) REVERT: O 101 VAL cc_start: 0.9444 (m) cc_final: 0.8897 (p) REVERT: O 105 GLU cc_start: 0.9302 (pt0) cc_final: 0.8971 (pt0) REVERT: P 44 LYS cc_start: 0.7207 (tptm) cc_final: 0.6840 (tppt) REVERT: P 59 LYS cc_start: 0.9374 (mmmm) cc_final: 0.9141 (mmmm) REVERT: P 61 PHE cc_start: 0.8791 (t80) cc_final: 0.8555 (t80) REVERT: P 88 TYR cc_start: 0.8350 (m-80) cc_final: 0.6763 (t80) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.2833 time to fit residues: 163.5069 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 : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 139 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 152 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** D 95 GLN E 93 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 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 = 0.3798 r_free = 0.3798 target = 0.077296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055330 restraints weight = 121498.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.056822 restraints weight = 60878.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057793 restraints weight = 38609.261| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21551 Z= 0.157 Angle : 0.636 7.610 31255 Z= 0.370 Chirality : 0.036 0.278 3561 Planarity : 0.005 0.073 2220 Dihedral : 32.572 178.063 6852 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.10 % Allowed : 1.24 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1219 helix: 1.40 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 75 PHE 0.034 0.002 PHE E 67 TYR 0.035 0.002 TYR L 88 ARG 0.012 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 1312) hydrogen bonds : angle 3.44227 ( 3284) covalent geometry : bond 0.00340 (21551) covalent geometry : angle 0.63606 (31255) *********************** 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 361 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 1.568 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 93 GLN cc_start: 0.8842 (tp40) cc_final: 0.8297 (tp40) REVERT: A 110 CYS cc_start: 0.9222 (m) cc_final: 0.8861 (t) REVERT: B 45 ARG cc_start: 0.8132 (tpt-90) cc_final: 0.7627 (tpt-90) REVERT: B 52 GLU cc_start: 0.8233 (mp0) cc_final: 0.7995 (mp0) REVERT: B 67 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7852 (ttp80) REVERT: B 74 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 84 MET cc_start: 0.8208 (mmm) cc_final: 0.7835 (mmm) REVERT: B 85 ASP cc_start: 0.8680 (m-30) cc_final: 0.8477 (m-30) REVERT: B 98 TYR cc_start: 0.8942 (m-10) cc_final: 0.8292 (m-10) REVERT: C 39 TYR cc_start: 0.8717 (m-80) cc_final: 0.7894 (m-80) REVERT: C 51 LEU cc_start: 0.9321 (tp) cc_final: 0.9118 (tp) REVERT: C 104 GLN cc_start: 0.8330 (mt0) cc_final: 0.7682 (mt0) REVERT: C 110 ASN cc_start: 0.9019 (t0) cc_final: 0.8745 (m110) REVERT: D 59 MET cc_start: 0.8927 (tpp) cc_final: 0.8520 (tpp) REVERT: D 62 MET cc_start: 0.8692 (mmm) cc_final: 0.8310 (mmp) REVERT: D 68 ASP cc_start: 0.8378 (t70) cc_final: 0.8116 (t0) REVERT: E 50 GLU cc_start: 0.8332 (mm-30) cc_final: 0.6748 (tp30) REVERT: E 54 TYR cc_start: 0.8363 (m-10) cc_final: 0.7096 (m-80) REVERT: E 62 ILE cc_start: 0.8413 (pt) cc_final: 0.7771 (pt) REVERT: E 82 LEU cc_start: 0.7951 (pt) cc_final: 0.7743 (pt) REVERT: E 93 GLN cc_start: 0.8383 (tt0) cc_final: 0.6470 (tp40) REVERT: E 94 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8684 (mt-10) REVERT: E 97 GLU cc_start: 0.7969 (pm20) cc_final: 0.7545 (pm20) REVERT: E 103 LEU cc_start: 0.9292 (tt) cc_final: 0.9069 (tt) REVERT: E 105 GLU cc_start: 0.8990 (tp30) cc_final: 0.8722 (tp30) REVERT: E 107 THR cc_start: 0.9285 (m) cc_final: 0.8964 (p) REVERT: E 113 HIS cc_start: 0.8342 (t-90) cc_final: 0.7799 (t-90) REVERT: F 27 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8215 (mp10) REVERT: F 44 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8062 (mtpt) REVERT: F 79 LYS cc_start: 0.7402 (mmtt) cc_final: 0.6677 (mmtt) REVERT: F 98 TYR cc_start: 0.9072 (m-10) cc_final: 0.8763 (m-10) REVERT: G 35 ARG cc_start: 0.8311 (mtm180) cc_final: 0.7776 (mtm110) REVERT: G 38 ASN cc_start: 0.8613 (m110) cc_final: 0.8179 (t0) REVERT: G 68 ASN cc_start: 0.9137 (m110) cc_final: 0.8846 (m-40) REVERT: G 95 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7983 (tmtt) REVERT: H 37 TYR cc_start: 0.8700 (m-80) cc_final: 0.7961 (m-80) REVERT: H 61 ILE cc_start: 0.8851 (mm) cc_final: 0.8256 (mt) REVERT: H 68 ASP cc_start: 0.8378 (t0) cc_final: 0.7833 (t0) REVERT: H 112 SER cc_start: 0.8867 (t) cc_final: 0.8606 (m) REVERT: K 65 LEU cc_start: 0.7585 (tp) cc_final: 0.7313 (tt) REVERT: K 103 LEU cc_start: 0.9276 (mt) cc_final: 0.8985 (mt) REVERT: K 107 THR cc_start: 0.9212 (p) cc_final: 0.8524 (p) REVERT: K 120 MET cc_start: 0.5779 (mtt) cc_final: 0.5101 (mtp) REVERT: K 123 ASP cc_start: 0.8687 (m-30) cc_final: 0.7828 (t0) REVERT: L 60 VAL cc_start: 0.9597 (t) cc_final: 0.9396 (t) REVERT: L 62 LEU cc_start: 0.9724 (mm) cc_final: 0.9406 (mm) REVERT: L 63 GLU cc_start: 0.8977 (pp20) cc_final: 0.8520 (pp20) REVERT: L 84 MET cc_start: 0.6033 (ppp) cc_final: 0.5717 (ppp) REVERT: M 56 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7360 (mt-10) REVERT: M 73 ASN cc_start: 0.9432 (t0) cc_final: 0.9122 (t0) REVERT: M 91 GLU cc_start: 0.8392 (pm20) cc_final: 0.8079 (pm20) REVERT: M 115 LEU cc_start: 0.6911 (tp) cc_final: 0.6670 (tp) REVERT: N 43 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8213 (tptp) REVERT: O 41 TYR cc_start: 0.6869 (m-80) cc_final: 0.6283 (m-80) REVERT: O 54 TYR cc_start: 0.8990 (m-80) cc_final: 0.8744 (m-10) REVERT: O 59 GLU cc_start: 0.8716 (mp0) cc_final: 0.7692 (tm-30) REVERT: O 76 GLN cc_start: 0.9029 (tt0) cc_final: 0.8578 (tp40) REVERT: O 96 CYS cc_start: 0.9331 (m) cc_final: 0.8438 (m) REVERT: O 101 VAL cc_start: 0.9429 (m) cc_final: 0.8885 (p) REVERT: O 105 GLU cc_start: 0.9299 (pt0) cc_final: 0.8948 (pt0) REVERT: P 44 LYS cc_start: 0.7047 (tptm) cc_final: 0.6712 (tppt) REVERT: P 53 GLU cc_start: 0.7991 (tt0) cc_final: 0.7550 (pt0) REVERT: P 59 LYS cc_start: 0.9375 (mmmm) cc_final: 0.9164 (mmmm) REVERT: P 61 PHE cc_start: 0.8789 (t80) cc_final: 0.8524 (t80) REVERT: P 72 TYR cc_start: 0.7935 (m-80) cc_final: 0.7520 (m-10) REVERT: P 84 MET cc_start: 0.7172 (tpp) cc_final: 0.6712 (tpp) REVERT: P 88 TYR cc_start: 0.8434 (m-80) cc_final: 0.7257 (t80) outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.2803 time to fit residues: 159.2231 Evaluate side-chains 297 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 ** 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** M 31 HIS ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN P 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.075179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053301 restraints weight = 118993.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.054793 restraints weight = 58587.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.055761 restraints weight = 37031.297| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21551 Z= 0.187 Angle : 0.651 9.831 31255 Z= 0.377 Chirality : 0.036 0.209 3561 Planarity : 0.005 0.068 2220 Dihedral : 32.703 177.935 6852 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1219 helix: 1.29 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 75 PHE 0.020 0.002 PHE F 61 TYR 0.034 0.002 TYR L 88 ARG 0.011 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05232 ( 1312) hydrogen bonds : angle 3.57274 ( 3284) covalent geometry : bond 0.00408 (21551) covalent geometry : angle 0.65132 (31255) *********************** 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 343 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8871 (tp40) cc_final: 0.8311 (tp40) REVERT: B 45 ARG cc_start: 0.8208 (tpt-90) cc_final: 0.7693 (tpt-90) REVERT: B 52 GLU cc_start: 0.8416 (mp0) cc_final: 0.8161 (mp0) REVERT: B 63 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8371 (tm-30) REVERT: B 67 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7899 (ttp80) REVERT: B 74 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7844 (tm-30) REVERT: B 84 MET cc_start: 0.8195 (mmm) cc_final: 0.7969 (tpp) REVERT: B 85 ASP cc_start: 0.8668 (m-30) cc_final: 0.8317 (m-30) REVERT: B 98 TYR cc_start: 0.8928 (m-10) cc_final: 0.8115 (m-80) REVERT: C 39 TYR cc_start: 0.8694 (m-80) cc_final: 0.7872 (m-80) REVERT: C 51 LEU cc_start: 0.9376 (tp) cc_final: 0.9102 (tt) REVERT: C 104 GLN cc_start: 0.8350 (mt0) cc_final: 0.7720 (mt0) REVERT: D 42 TYR cc_start: 0.8537 (t80) cc_final: 0.8212 (t80) REVERT: D 62 MET cc_start: 0.8675 (mmm) cc_final: 0.8324 (mmp) REVERT: D 68 ASP cc_start: 0.8437 (t70) cc_final: 0.8154 (t0) REVERT: E 50 GLU cc_start: 0.8308 (mm-30) cc_final: 0.6639 (tp30) REVERT: E 54 TYR cc_start: 0.8434 (m-10) cc_final: 0.7227 (m-80) REVERT: E 82 LEU cc_start: 0.7979 (pt) cc_final: 0.7715 (pt) REVERT: E 94 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8750 (mt-10) REVERT: E 105 GLU cc_start: 0.8879 (tp30) cc_final: 0.8648 (tp30) REVERT: E 107 THR cc_start: 0.9221 (m) cc_final: 0.8934 (p) REVERT: F 27 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8285 (mp10) REVERT: F 44 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8076 (mtpt) REVERT: F 79 LYS cc_start: 0.7286 (mmtt) cc_final: 0.6533 (mmtt) REVERT: F 85 ASP cc_start: 0.8072 (m-30) cc_final: 0.7682 (m-30) REVERT: F 88 TYR cc_start: 0.8463 (m-10) cc_final: 0.8167 (m-80) REVERT: G 38 ASN cc_start: 0.8696 (m110) cc_final: 0.8438 (t0) REVERT: G 68 ASN cc_start: 0.9093 (m110) cc_final: 0.8781 (m-40) REVERT: G 95 LYS cc_start: 0.8357 (ttmt) cc_final: 0.7972 (tmtt) REVERT: H 37 TYR cc_start: 0.8816 (m-80) cc_final: 0.7945 (m-80) REVERT: H 68 ASP cc_start: 0.8554 (t0) cc_final: 0.8085 (t0) REVERT: H 112 SER cc_start: 0.8928 (t) cc_final: 0.8621 (m) REVERT: K 65 LEU cc_start: 0.7658 (tp) cc_final: 0.7384 (tt) REVERT: K 90 MET cc_start: 0.8510 (mmp) cc_final: 0.8282 (mmp) REVERT: K 103 LEU cc_start: 0.9268 (mt) cc_final: 0.8990 (mt) REVERT: K 107 THR cc_start: 0.9210 (p) cc_final: 0.8531 (p) REVERT: K 120 MET cc_start: 0.5310 (mtt) cc_final: 0.4754 (mtp) REVERT: K 123 ASP cc_start: 0.8719 (m-30) cc_final: 0.7899 (t0) REVERT: K 125 GLN cc_start: 0.8833 (pm20) cc_final: 0.8550 (pm20) REVERT: L 62 LEU cc_start: 0.9703 (mm) cc_final: 0.9396 (mm) REVERT: L 63 GLU cc_start: 0.8788 (pp20) cc_final: 0.8315 (pp20) REVERT: L 74 GLU cc_start: 0.9229 (tm-30) cc_final: 0.9016 (tm-30) REVERT: L 88 TYR cc_start: 0.5383 (m-80) cc_final: 0.5000 (m-10) REVERT: M 64 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8295 (tm-30) REVERT: M 73 ASN cc_start: 0.9394 (t0) cc_final: 0.9034 (t0) REVERT: M 115 LEU cc_start: 0.6940 (tp) cc_final: 0.6690 (tp) REVERT: N 43 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8075 (tptp) REVERT: N 45 LEU cc_start: 0.8774 (tt) cc_final: 0.8536 (tt) REVERT: N 99 ARG cc_start: 0.8548 (ptm160) cc_final: 0.7735 (ptt90) REVERT: O 41 TYR cc_start: 0.6735 (m-80) cc_final: 0.6330 (m-80) REVERT: O 54 TYR cc_start: 0.9001 (m-80) cc_final: 0.8747 (m-10) REVERT: O 59 GLU cc_start: 0.8730 (mp0) cc_final: 0.7699 (tm-30) REVERT: O 76 GLN cc_start: 0.9041 (tt0) cc_final: 0.8562 (tp40) REVERT: O 96 CYS cc_start: 0.9312 (m) cc_final: 0.8409 (m) REVERT: O 101 VAL cc_start: 0.9442 (m) cc_final: 0.8910 (p) REVERT: O 105 GLU cc_start: 0.9310 (pt0) cc_final: 0.8961 (pt0) REVERT: O 119 ILE cc_start: 0.8788 (pt) cc_final: 0.8557 (pt) REVERT: O 120 MET cc_start: 0.7919 (tmm) cc_final: 0.7246 (ppp) REVERT: P 44 LYS cc_start: 0.7029 (tptm) cc_final: 0.6696 (tppt) REVERT: P 59 LYS cc_start: 0.9363 (mmmm) cc_final: 0.9136 (mmmm) REVERT: P 84 MET cc_start: 0.7328 (tpp) cc_final: 0.6830 (tpp) REVERT: P 88 TYR cc_start: 0.8424 (m-80) cc_final: 0.7233 (t80) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2719 time to fit residues: 147.6965 Evaluate side-chains 286 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 138 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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** C 110 ASN 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** M 31 HIS M 82 HIS O 68 GLN P 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.073878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.051896 restraints weight = 119850.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053379 restraints weight = 58639.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054314 restraints weight = 36952.319| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21551 Z= 0.213 Angle : 0.695 13.784 31255 Z= 0.398 Chirality : 0.038 0.193 3561 Planarity : 0.005 0.061 2220 Dihedral : 33.020 178.379 6852 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1219 helix: 1.07 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.61 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS B 75 PHE 0.021 0.002 PHE F 61 TYR 0.035 0.002 TYR L 88 ARG 0.012 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05836 ( 1312) hydrogen bonds : angle 3.83802 ( 3284) covalent geometry : bond 0.00464 (21551) covalent geometry : angle 0.69453 (31255) ********************** 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 331 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.357 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: 0.8324 (pm20) cc_final: 0.8123 (pm20) REVERT: A 93 GLN cc_start: 0.8984 (tp40) cc_final: 0.8424 (tp40) REVERT: A 105 GLU cc_start: 0.7689 (pp20) cc_final: 0.7481 (pp20) REVERT: A 106 ASP cc_start: 0.8872 (m-30) cc_final: 0.8203 (m-30) REVERT: A 110 CYS cc_start: 0.8913 (t) cc_final: 0.7634 (t) REVERT: A 123 ASP cc_start: 0.8601 (m-30) cc_final: 0.8233 (t0) REVERT: B 45 ARG cc_start: 0.8212 (tpt-90) cc_final: 0.7725 (tpt-90) REVERT: B 52 GLU cc_start: 0.8474 (mp0) cc_final: 0.8194 (mp0) REVERT: B 63 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8416 (tm-30) REVERT: B 67 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7935 (ttp80) REVERT: B 74 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 85 ASP cc_start: 0.8606 (m-30) cc_final: 0.8353 (m-30) REVERT: B 98 TYR cc_start: 0.8897 (m-10) cc_final: 0.8558 (m-80) REVERT: C 39 TYR cc_start: 0.8819 (m-80) cc_final: 0.8216 (m-80) REVERT: C 104 GLN cc_start: 0.8333 (mt0) cc_final: 0.7451 (mt0) REVERT: C 112 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7828 (mm-40) REVERT: D 42 TYR cc_start: 0.8677 (t80) cc_final: 0.8332 (t80) REVERT: D 44 VAL cc_start: 0.9509 (t) cc_final: 0.9304 (p) REVERT: D 62 MET cc_start: 0.8449 (mmm) cc_final: 0.8169 (mmp) REVERT: D 68 ASP cc_start: 0.8470 (t70) cc_final: 0.8244 (t0) REVERT: E 50 GLU cc_start: 0.8295 (mm-30) cc_final: 0.6757 (tp30) REVERT: E 54 TYR cc_start: 0.8457 (m-10) cc_final: 0.7188 (m-80) REVERT: E 62 ILE cc_start: 0.7672 (pt) cc_final: 0.7419 (pt) REVERT: E 82 LEU cc_start: 0.8033 (pt) cc_final: 0.7794 (pt) REVERT: E 105 GLU cc_start: 0.8867 (tp30) cc_final: 0.8663 (tp30) REVERT: E 107 THR cc_start: 0.9201 (m) cc_final: 0.8995 (p) REVERT: E 108 ASN cc_start: 0.9233 (t0) cc_final: 0.8852 (t0) REVERT: E 109 LEU cc_start: 0.9277 (mt) cc_final: 0.9070 (mt) REVERT: E 112 ILE cc_start: 0.9129 (pt) cc_final: 0.8893 (pt) REVERT: F 43 VAL cc_start: 0.8985 (t) cc_final: 0.8752 (t) REVERT: F 79 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6533 (mmtt) REVERT: F 85 ASP cc_start: 0.8103 (m-30) cc_final: 0.7716 (m-30) REVERT: F 88 TYR cc_start: 0.8408 (m-10) cc_final: 0.8038 (m-80) REVERT: G 38 ASN cc_start: 0.8817 (m110) cc_final: 0.8457 (t0) REVERT: G 68 ASN cc_start: 0.9097 (m110) cc_final: 0.8700 (t0) REVERT: G 95 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7854 (tmtt) REVERT: H 37 TYR cc_start: 0.8870 (m-80) cc_final: 0.8064 (m-80) REVERT: H 68 ASP cc_start: 0.8651 (t0) cc_final: 0.8403 (t70) REVERT: H 111 VAL cc_start: 0.9650 (m) cc_final: 0.9435 (p) REVERT: H 112 SER cc_start: 0.9012 (t) cc_final: 0.8776 (p) REVERT: K 65 LEU cc_start: 0.7678 (tp) cc_final: 0.7411 (tt) REVERT: K 90 MET cc_start: 0.8515 (mmp) cc_final: 0.8288 (mmp) REVERT: K 103 LEU cc_start: 0.9212 (mt) cc_final: 0.8961 (mt) REVERT: K 107 THR cc_start: 0.9160 (p) cc_final: 0.8577 (p) REVERT: K 120 MET cc_start: 0.5854 (mtt) cc_final: 0.5224 (mtp) REVERT: K 123 ASP cc_start: 0.8586 (m-30) cc_final: 0.7917 (t0) REVERT: L 62 LEU cc_start: 0.9703 (mm) cc_final: 0.9399 (mm) REVERT: L 63 GLU cc_start: 0.8917 (pp20) cc_final: 0.8478 (pp20) REVERT: L 88 TYR cc_start: 0.5011 (m-80) cc_final: 0.4808 (m-10) REVERT: M 64 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8175 (tm-30) REVERT: M 91 GLU cc_start: 0.8452 (pm20) cc_final: 0.8015 (pm20) REVERT: N 43 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8186 (tptp) REVERT: O 54 TYR cc_start: 0.9003 (m-80) cc_final: 0.8726 (m-10) REVERT: O 59 GLU cc_start: 0.8707 (mp0) cc_final: 0.7646 (tm-30) REVERT: O 67 PHE cc_start: 0.8810 (t80) cc_final: 0.8494 (t80) REVERT: O 76 GLN cc_start: 0.9027 (tt0) cc_final: 0.8525 (tp40) REVERT: O 84 PHE cc_start: 0.6393 (m-80) cc_final: 0.4913 (p90) REVERT: O 96 CYS cc_start: 0.9465 (m) cc_final: 0.8602 (m) REVERT: O 101 VAL cc_start: 0.9482 (m) cc_final: 0.8951 (p) REVERT: O 105 GLU cc_start: 0.9325 (pt0) cc_final: 0.9007 (pt0) REVERT: P 44 LYS cc_start: 0.7020 (tptm) cc_final: 0.6671 (tppt) REVERT: P 59 LYS cc_start: 0.9359 (mmmm) cc_final: 0.9139 (mmmm) REVERT: P 84 MET cc_start: 0.7283 (tpp) cc_final: 0.6788 (tpp) REVERT: P 88 TYR cc_start: 0.8392 (m-80) cc_final: 0.7035 (t80) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2797 time to fit residues: 146.9891 Evaluate side-chains 274 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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** C 31 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 93 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS O 68 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 = 0.3712 r_free = 0.3712 target = 0.073120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051667 restraints weight = 122223.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053127 restraints weight = 61026.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.053783 restraints weight = 34294.293| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.7164 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= 0.236 Angle : 0.716 12.249 31255 Z= 0.411 Chirality : 0.038 0.279 3561 Planarity : 0.005 0.067 2220 Dihedral : 33.243 179.507 6852 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1219 helix: 0.87 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.89 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 75 PHE 0.020 0.002 PHE F 61 TYR 0.034 0.003 TYR B 88 ARG 0.012 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.06346 ( 1312) hydrogen bonds : angle 4.00377 ( 3284) covalent geometry : bond 0.00514 (21551) covalent geometry : angle 0.71603 (31255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6207.40 seconds wall clock time: 109 minutes 7.48 seconds (6547.48 seconds total)