Starting phenix.real_space_refine on Tue Jun 17 03:52:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3f_38880/06_2025/8y3f_38880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3f_38880/06_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_38880/06_2025/8y3f_38880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3f_38880/06_2025/8y3f_38880.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3f_38880/06_2025/8y3f_38880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3f_38880/06_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-5710/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: 12.96, per 1000 atoms: 0.64 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: 4.99 Conformation dependent library (CDL) restraints added in 1.5 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: 10.46 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: 8.93 Time building geometry restraints manager: 5.99 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: 32.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 58.430 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.630 ------------------------------------------------------------------------------- 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 : 1.402 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: 0.4240 time to fit residues: 353.7693 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 : 1.528 ------------------------------------------------------------------------------- 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 = 126157.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061633 restraints weight = 73960.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.061971 restraints weight = 48872.963| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 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 = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 1.520 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: 0.9218 (mt) cc_final: 0.8990 (mm) REVERT: A 76 GLN cc_start: 0.8646 (tp40) cc_final: 0.8334 (tp40) REVERT: A 84 PHE cc_start: 0.8383 (m-80) cc_final: 0.8125 (m-80) REVERT: A 110 CYS cc_start: 0.9265 (m) cc_final: 0.9025 (m) REVERT: B 40 ARG cc_start: 0.9172 (mtp180) cc_final: 0.8952 (tpp80) REVERT: B 45 ARG cc_start: 0.7489 (mtp85) cc_final: 0.7229 (tpt-90) REVERT: B 59 LYS cc_start: 0.9049 (tptt) cc_final: 0.8511 (tptp) REVERT: B 63 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 74 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 98 TYR cc_start: 0.8807 (m-10) cc_final: 0.8555 (m-10) REVERT: C 25 PHE cc_start: 0.8622 (m-80) cc_final: 0.7886 (m-10) REVERT: C 104 GLN cc_start: 0.8351 (mt0) cc_final: 0.7832 (mt0) REVERT: C 110 ASN cc_start: 0.9135 (t0) cc_final: 0.8705 (m110) REVERT: D 34 LYS cc_start: 0.7488 (tptp) cc_final: 0.7214 (tppt) REVERT: D 42 TYR cc_start: 0.8496 (t80) cc_final: 0.8293 (t80) REVERT: D 44 VAL cc_start: 0.9448 (t) cc_final: 0.9093 (p) REVERT: D 68 ASP cc_start: 0.8420 (t70) cc_final: 0.8130 (t0) REVERT: D 82 HIS cc_start: 0.8215 (t-90) cc_final: 0.7905 (t70) REVERT: D 95 GLN cc_start: 0.8527 (tt0) cc_final: 0.8209 (tt0) REVERT: E 46 VAL cc_start: 0.7896 (t) cc_final: 0.7659 (t) REVERT: E 54 TYR cc_start: 0.8353 (m-10) cc_final: 0.7532 (m-80) REVERT: E 93 GLN cc_start: 0.9150 (tt0) cc_final: 0.8497 (tm-30) REVERT: E 106 ASP cc_start: 0.8659 (m-30) cc_final: 0.8309 (m-30) REVERT: F 44 LYS cc_start: 0.8697 (ttpp) cc_final: 0.7878 (mtpt) REVERT: F 64 ASN cc_start: 0.8936 (m110) cc_final: 0.8651 (m110) REVERT: F 79 LYS cc_start: 0.7322 (mmtt) cc_final: 0.6738 (tptp) REVERT: F 88 TYR cc_start: 0.8659 (m-80) cc_final: 0.8165 (m-80) REVERT: G 35 ARG cc_start: 0.8202 (mtm180) cc_final: 0.7793 (ptp90) REVERT: G 38 ASN cc_start: 0.8330 (m110) cc_final: 0.8052 (m110) REVERT: H 68 ASP cc_start: 0.8667 (t0) cc_final: 0.8023 (t0) REVERT: H 94 ILE cc_start: 0.9508 (mm) cc_final: 0.9269 (mm) REVERT: H 106 LEU cc_start: 0.9570 (mt) cc_final: 0.9078 (mt) REVERT: H 112 SER cc_start: 0.9159 (t) cc_final: 0.8866 (p) REVERT: K 106 ASP cc_start: 0.9411 (m-30) cc_final: 0.9142 (m-30) REVERT: L 64 ASN cc_start: 0.9450 (t0) cc_final: 0.9194 (t0) REVERT: L 85 ASP cc_start: 0.5432 (m-30) cc_final: 0.5204 (m-30) REVERT: M 58 LEU cc_start: 0.8898 (mp) cc_final: 0.8639 (pp) REVERT: M 64 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8074 (tm-30) REVERT: M 84 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8621 (tm-30) REVERT: M 107 VAL cc_start: 0.8986 (t) cc_final: 0.8746 (p) REVERT: N 44 VAL cc_start: 0.9181 (t) cc_final: 0.8926 (t) REVERT: N 68 ASP cc_start: 0.8628 (t70) cc_final: 0.8138 (t0) REVERT: N 71 GLU cc_start: 0.8613 (pp20) cc_final: 0.8180 (pp20) REVERT: N 102 LEU cc_start: 0.8459 (mm) cc_final: 0.8245 (mm) REVERT: O 41 TYR cc_start: 0.6086 (m-80) cc_final: 0.5589 (m-80) REVERT: O 60 LEU cc_start: 0.5561 (mp) cc_final: 0.4916 (mp) REVERT: O 61 LEU cc_start: 0.8599 (mt) cc_final: 0.8110 (mp) REVERT: O 65 LEU cc_start: 0.7951 (tp) cc_final: 0.7648 (tp) REVERT: O 68 GLN cc_start: 0.9111 (mt0) cc_final: 0.8900 (mt0) REVERT: O 76 GLN cc_start: 0.9287 (tt0) cc_final: 0.8777 (tp40) REVERT: O 96 CYS cc_start: 0.9317 (m) cc_final: 0.9027 (m) REVERT: O 105 GLU cc_start: 0.9272 (pt0) cc_final: 0.8975 (pt0) REVERT: P 57 VAL cc_start: 0.9438 (t) cc_final: 0.9217 (p) REVERT: P 84 MET cc_start: 0.6731 (tpp) cc_final: 0.6531 (tpp) REVERT: P 88 TYR cc_start: 0.7568 (m-80) cc_final: 0.7175 (t80) REVERT: P 93 GLN cc_start: 0.8822 (tt0) cc_final: 0.8300 (tm-30) outliers start: 1 outliers final: 0 residues processed: 418 average time/residue: 0.3307 time to fit residues: 206.9905 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 : 1.587 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.3726 r_free = 0.3726 target = 0.074191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.052208 restraints weight = 118746.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053664 restraints weight = 59595.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.054602 restraints weight = 37817.734| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21551 Z= 0.248 Angle : 0.687 10.195 31255 Z= 0.399 Chirality : 0.038 0.203 3561 Planarity : 0.006 0.068 2220 Dihedral : 33.025 179.297 6852 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.19 % Allowed : 5.54 % Favored : 94.26 % 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: 1.25 (0.22), residues: 1219 helix: 1.26 (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 0.025 0.003 TYR M 57 ARG 0.010 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.06241 ( 1312) hydrogen bonds : angle 3.87768 ( 3284) covalent geometry : bond 0.00540 (21551) covalent geometry : angle 0.68670 (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 393 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 391 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8325 (m-80) cc_final: 0.8004 (m-10) REVERT: A 93 GLN cc_start: 0.9298 (tt0) cc_final: 0.8536 (tp40) REVERT: A 110 CYS cc_start: 0.9255 (m) cc_final: 0.8988 (m) REVERT: A 120 MET cc_start: 0.9197 (mtm) cc_final: 0.8957 (mtp) REVERT: B 40 ARG cc_start: 0.8939 (mtp180) cc_final: 0.8632 (tpp80) REVERT: B 52 GLU cc_start: 0.8678 (mp0) cc_final: 0.8270 (mp0) REVERT: B 74 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7966 (tm-30) REVERT: B 88 TYR cc_start: 0.8007 (m-10) cc_final: 0.7092 (m-10) REVERT: B 98 TYR cc_start: 0.8881 (m-10) cc_final: 0.8489 (m-10) REVERT: C 39 TYR cc_start: 0.8948 (m-80) cc_final: 0.8286 (m-80) REVERT: D 42 TYR cc_start: 0.8637 (t80) cc_final: 0.8423 (t80) REVERT: D 44 VAL cc_start: 0.9478 (t) cc_final: 0.9131 (p) REVERT: D 62 MET cc_start: 0.8477 (mmm) cc_final: 0.8141 (mmp) REVERT: D 68 ASP cc_start: 0.8567 (t70) cc_final: 0.8317 (t0) REVERT: D 82 HIS cc_start: 0.8392 (t-90) cc_final: 0.8146 (t70) REVERT: D 89 ILE cc_start: 0.8853 (mt) cc_final: 0.8493 (tt) REVERT: D 100 LEU cc_start: 0.9198 (mm) cc_final: 0.8918 (mm) REVERT: D 108 LYS cc_start: 0.9235 (mttm) cc_final: 0.8916 (mtpt) REVERT: E 50 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7780 (tp30) REVERT: E 59 GLU cc_start: 0.7908 (pm20) cc_final: 0.7659 (pm20) REVERT: E 62 ILE cc_start: 0.7931 (pt) cc_final: 0.6949 (pt) REVERT: E 81 ASP cc_start: 0.7591 (t0) cc_final: 0.7267 (t0) REVERT: E 92 LEU cc_start: 0.9408 (mt) cc_final: 0.9193 (mt) REVERT: E 93 GLN cc_start: 0.9051 (tt0) cc_final: 0.8148 (tp40) REVERT: E 103 LEU cc_start: 0.9323 (tt) cc_final: 0.9021 (tt) REVERT: E 106 ASP cc_start: 0.8762 (m-30) cc_final: 0.8511 (m-30) REVERT: F 79 LYS cc_start: 0.7375 (mmtt) cc_final: 0.7012 (tptt) REVERT: F 88 TYR cc_start: 0.8551 (m-10) cc_final: 0.8205 (m-80) REVERT: G 35 ARG cc_start: 0.8263 (mtm180) cc_final: 0.7576 (ptp90) REVERT: G 38 ASN cc_start: 0.8495 (m110) cc_final: 0.8241 (t0) REVERT: G 68 ASN cc_start: 0.9217 (m110) cc_final: 0.8868 (m-40) REVERT: G 95 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7770 (tmtt) REVERT: H 37 TYR cc_start: 0.8952 (m-80) cc_final: 0.7762 (m-80) REVERT: H 54 ILE cc_start: 0.8724 (mp) cc_final: 0.8332 (mp) REVERT: H 68 ASP cc_start: 0.8882 (t0) cc_final: 0.8570 (t0) REVERT: H 112 SER cc_start: 0.9189 (t) cc_final: 0.8874 (p) REVERT: K 120 MET cc_start: 0.4997 (mtt) cc_final: 0.4794 (mtp) REVERT: M 84 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8522 (tm-30) REVERT: N 102 LEU cc_start: 0.8177 (mm) cc_final: 0.7940 (mm) REVERT: O 53 ARG cc_start: 0.9248 (tpp-160) cc_final: 0.8726 (ptm160) REVERT: O 54 TYR cc_start: 0.8965 (m-80) cc_final: 0.8115 (m-80) REVERT: O 61 LEU cc_start: 0.8045 (mt) cc_final: 0.7721 (mp) REVERT: O 64 LYS cc_start: 0.8506 (pptt) cc_final: 0.8222 (pptt) REVERT: O 65 LEU cc_start: 0.8157 (tp) cc_final: 0.7727 (tp) REVERT: O 68 GLN cc_start: 0.9092 (mt0) cc_final: 0.8800 (mt0) REVERT: O 76 GLN cc_start: 0.9057 (tt0) cc_final: 0.8544 (tp40) REVERT: O 96 CYS cc_start: 0.9513 (m) cc_final: 0.9298 (m) REVERT: O 99 TYR cc_start: 0.8345 (t80) cc_final: 0.7813 (t80) REVERT: O 101 VAL cc_start: 0.9460 (m) cc_final: 0.8921 (p) REVERT: O 105 GLU cc_start: 0.9254 (pt0) cc_final: 0.9001 (pt0) REVERT: P 44 LYS cc_start: 0.7491 (tttt) cc_final: 0.7170 (ttmm) REVERT: P 57 VAL cc_start: 0.9344 (t) cc_final: 0.9130 (p) REVERT: P 61 PHE cc_start: 0.9033 (t80) cc_final: 0.8561 (t80) REVERT: P 84 MET cc_start: 0.7368 (tpp) cc_final: 0.7124 (tpp) REVERT: P 93 GLN cc_start: 0.8519 (tt0) cc_final: 0.8085 (tm-30) outliers start: 2 outliers final: 0 residues processed: 392 average time/residue: 0.3179 time to fit residues: 188.7740 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 : 1.418 ------------------------------------------------------------------------------- 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: 20.0000 chunk 154 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.075859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.054023 restraints weight = 117947.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.055570 restraints weight = 57043.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.056559 restraints weight = 35615.689| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 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 = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21551 Z= 0.163 Angle : 0.617 7.711 31255 Z= 0.362 Chirality : 0.036 0.162 3561 Planarity : 0.005 0.066 2220 Dihedral : 32.756 179.424 6852 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.23), residues: 1219 helix: 1.49 (0.16), residues: 933 sheet: None (None), residues: 0 loop : -0.32 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 82 PHE 0.019 0.002 PHE N 65 TYR 0.028 0.002 TYR C 57 ARG 0.009 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04762 ( 1312) hydrogen bonds : angle 3.48859 ( 3284) covalent geometry : bond 0.00355 (21551) covalent geometry : angle 0.61695 (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 : 1.544 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: 0.8985 (t) cc_final: 0.7794 (p) REVERT: A 80 THR cc_start: 0.8408 (t) cc_final: 0.8161 (m) REVERT: A 84 PHE cc_start: 0.8151 (m-80) cc_final: 0.7844 (m-10) REVERT: A 110 CYS cc_start: 0.9252 (m) cc_final: 0.8810 (t) REVERT: A 120 MET cc_start: 0.9224 (mtm) cc_final: 0.8876 (mtp) REVERT: A 123 ASP cc_start: 0.8215 (m-30) cc_final: 0.7651 (m-30) REVERT: B 37 LEU cc_start: 0.9402 (mm) cc_final: 0.9191 (mm) REVERT: B 40 ARG cc_start: 0.8877 (mtp180) cc_final: 0.8542 (tpp80) REVERT: B 52 GLU cc_start: 0.8689 (mp0) cc_final: 0.8400 (mp0) REVERT: B 63 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8316 (tm-30) REVERT: B 67 ARG cc_start: 0.8871 (tpp80) cc_final: 0.8533 (tpp80) REVERT: B 68 ASP cc_start: 0.9145 (m-30) cc_final: 0.8837 (m-30) REVERT: B 74 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 79 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7159 (tptm) REVERT: B 88 TYR cc_start: 0.7617 (m-10) cc_final: 0.7339 (m-10) REVERT: B 98 TYR cc_start: 0.8874 (m-10) cc_final: 0.8389 (m-10) REVERT: C 39 TYR cc_start: 0.8988 (m-80) cc_final: 0.8249 (m-80) REVERT: C 104 GLN cc_start: 0.8657 (mt0) cc_final: 0.7803 (mm-40) REVERT: C 110 ASN cc_start: 0.8849 (t0) cc_final: 0.8553 (m110) REVERT: C 111 ILE cc_start: 0.9061 (mt) cc_final: 0.8854 (mm) REVERT: C 112 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7770 (mm-40) REVERT: D 44 VAL cc_start: 0.9386 (t) cc_final: 0.9025 (p) REVERT: D 68 ASP cc_start: 0.8505 (t70) cc_final: 0.8264 (t0) REVERT: D 96 THR cc_start: 0.9242 (t) cc_final: 0.8856 (p) REVERT: D 100 LEU cc_start: 0.9069 (mm) cc_final: 0.8763 (mm) REVERT: D 108 LYS cc_start: 0.9226 (mttm) cc_final: 0.8959 (mtmt) REVERT: E 50 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7739 (tp30) REVERT: E 109 LEU cc_start: 0.9077 (mp) cc_final: 0.8477 (mt) REVERT: F 37 LEU cc_start: 0.8956 (mm) cc_final: 0.8715 (mm) REVERT: F 44 LYS cc_start: 0.8734 (mtpt) cc_final: 0.8136 (mtpp) REVERT: G 35 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7809 (mtm110) REVERT: G 38 ASN cc_start: 0.8307 (m110) cc_final: 0.7980 (t0) REVERT: G 68 ASN cc_start: 0.9175 (m110) cc_final: 0.8903 (t0) REVERT: G 95 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7999 (tmtt) REVERT: G 101 THR cc_start: 0.8976 (t) cc_final: 0.8595 (p) REVERT: H 37 TYR cc_start: 0.8861 (m-80) cc_final: 0.7895 (m-10) REVERT: H 54 ILE cc_start: 0.8258 (mp) cc_final: 0.7839 (mp) REVERT: H 68 ASP cc_start: 0.8790 (t0) cc_final: 0.7940 (t0) REVERT: H 94 ILE cc_start: 0.9482 (mm) cc_final: 0.9272 (mm) REVERT: H 112 SER cc_start: 0.9103 (t) cc_final: 0.8733 (p) REVERT: K 90 MET cc_start: 0.8712 (mpp) cc_final: 0.8404 (mpp) REVERT: K 120 MET cc_start: 0.5293 (mtt) cc_final: 0.5089 (mtp) REVERT: K 123 ASP cc_start: 0.8656 (m-30) cc_final: 0.8296 (m-30) REVERT: M 25 PHE cc_start: 0.7526 (m-10) cc_final: 0.6842 (m-10) REVERT: M 49 VAL cc_start: 0.8025 (t) cc_final: 0.7678 (p) REVERT: M 56 GLU cc_start: 0.8331 (tt0) cc_final: 0.7327 (tt0) REVERT: M 64 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8196 (tm-30) REVERT: O 41 TYR cc_start: 0.6280 (m-80) cc_final: 0.5504 (m-10) REVERT: O 54 TYR cc_start: 0.8948 (m-80) cc_final: 0.8109 (m-80) REVERT: O 61 LEU cc_start: 0.8717 (mt) cc_final: 0.8299 (mp) REVERT: O 64 LYS cc_start: 0.8515 (pptt) cc_final: 0.8215 (pptt) REVERT: O 65 LEU cc_start: 0.8183 (tp) cc_final: 0.7751 (tp) REVERT: O 76 GLN cc_start: 0.9065 (tt0) cc_final: 0.8540 (tp40) REVERT: O 101 VAL cc_start: 0.9417 (m) cc_final: 0.8895 (p) REVERT: O 105 GLU cc_start: 0.9254 (pt0) cc_final: 0.8946 (pt0) REVERT: P 44 LYS cc_start: 0.7493 (tttt) cc_final: 0.7104 (ttmm) REVERT: P 61 PHE cc_start: 0.8899 (t80) cc_final: 0.8654 (t80) REVERT: P 84 MET cc_start: 0.7351 (tpp) cc_final: 0.7094 (tpp) REVERT: P 88 TYR cc_start: 0.8093 (m-80) cc_final: 0.6763 (t80) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.3772 time to fit residues: 234.1001 Evaluate side-chains 316 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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: 6.9990 chunk 140 optimal weight: 0.9990 chunk 9 optimal weight: 0.0470 chunk 60 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- 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** B 75 HIS C 110 ASN C 112 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.077410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.055031 restraints weight = 122097.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.056532 restraints weight = 60899.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.057501 restraints weight = 38962.631| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- 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: 3 | |-----------------------------------------------------------------------------| |-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: 0.7607 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21551 Z= 0.157 Angle : 0.615 7.955 31255 Z= 0.361 Chirality : 0.035 0.223 3561 Planarity : 0.005 0.055 2220 Dihedral : 32.635 179.936 6852 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.62 (0.23), residues: 1219 helix: 1.55 (0.16), residues: 934 sheet: None (None), residues: 0 loop : -0.39 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.016 0.002 PHE O 67 TYR 0.037 0.002 TYR L 88 ARG 0.009 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 1312) hydrogen bonds : angle 3.43979 ( 3284) covalent geometry : bond 0.00340 (21551) covalent geometry : angle 0.61505 (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 397 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8142 (m-80) cc_final: 0.7902 (m-10) REVERT: A 93 GLN cc_start: 0.9130 (tp40) cc_final: 0.8217 (tp40) REVERT: A 110 CYS cc_start: 0.9219 (m) cc_final: 0.8795 (t) REVERT: A 123 ASP cc_start: 0.7961 (m-30) cc_final: 0.7397 (m-30) REVERT: B 37 LEU cc_start: 0.9437 (mm) cc_final: 0.9225 (mm) REVERT: B 40 ARG cc_start: 0.8915 (mtp180) cc_final: 0.8474 (tpp80) REVERT: B 45 ARG cc_start: 0.7833 (tpt-90) cc_final: 0.7220 (tpt-90) REVERT: B 63 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 67 ARG cc_start: 0.8624 (tpp80) cc_final: 0.8357 (ttm110) REVERT: B 68 ASP cc_start: 0.9143 (m-30) cc_final: 0.8681 (m-30) REVERT: B 74 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 79 LYS cc_start: 0.7744 (mtmm) cc_final: 0.7241 (tptm) REVERT: B 98 TYR cc_start: 0.8831 (m-10) cc_final: 0.8315 (m-10) REVERT: C 39 TYR cc_start: 0.8968 (m-80) cc_final: 0.8353 (m-80) REVERT: C 104 GLN cc_start: 0.8424 (mt0) cc_final: 0.7785 (mm-40) REVERT: D 44 VAL cc_start: 0.9395 (t) cc_final: 0.9004 (p) REVERT: D 62 MET cc_start: 0.8720 (mmm) cc_final: 0.8443 (mmp) REVERT: D 89 ILE cc_start: 0.9015 (tt) cc_final: 0.8733 (mt) REVERT: D 96 THR cc_start: 0.9283 (t) cc_final: 0.9015 (p) REVERT: D 100 LEU cc_start: 0.9012 (mm) cc_final: 0.8794 (mm) REVERT: D 105 GLU cc_start: 0.8244 (pm20) cc_final: 0.8003 (pm20) REVERT: E 50 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7888 (tp30) REVERT: E 67 PHE cc_start: 0.8181 (t80) cc_final: 0.7887 (t80) REVERT: E 82 LEU cc_start: 0.7671 (pt) cc_final: 0.7432 (pt) REVERT: E 94 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8546 (mt-10) REVERT: E 103 LEU cc_start: 0.9336 (tt) cc_final: 0.9130 (tt) REVERT: E 107 THR cc_start: 0.9285 (m) cc_final: 0.9003 (p) REVERT: E 109 LEU cc_start: 0.9008 (mp) cc_final: 0.8621 (mt) REVERT: E 113 HIS cc_start: 0.8522 (t70) cc_final: 0.7988 (t70) REVERT: F 44 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8100 (mtpp) REVERT: F 79 LYS cc_start: 0.7271 (mmtt) cc_final: 0.6530 (mmtt) REVERT: F 88 TYR cc_start: 0.7982 (m-80) cc_final: 0.7640 (m-10) REVERT: F 98 TYR cc_start: 0.8958 (m-10) cc_final: 0.8677 (m-10) REVERT: G 35 ARG cc_start: 0.8383 (mtm180) cc_final: 0.7790 (mtm110) REVERT: G 38 ASN cc_start: 0.8297 (m110) cc_final: 0.8040 (t0) REVERT: G 68 ASN cc_start: 0.9175 (m110) cc_final: 0.8889 (m-40) REVERT: G 95 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7986 (tmtt) REVERT: H 37 TYR cc_start: 0.8791 (m-80) cc_final: 0.7947 (m-10) REVERT: H 61 ILE cc_start: 0.8967 (mm) cc_final: 0.8491 (mt) REVERT: H 68 ASP cc_start: 0.8681 (t0) cc_final: 0.7795 (t0) REVERT: H 112 SER cc_start: 0.9062 (t) cc_final: 0.8790 (p) REVERT: K 94 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7995 (mm-30) REVERT: K 103 LEU cc_start: 0.9308 (mt) cc_final: 0.9030 (mt) REVERT: K 120 MET cc_start: 0.5247 (mtt) cc_final: 0.4839 (mtp) REVERT: K 123 ASP cc_start: 0.8642 (m-30) cc_final: 0.8298 (m-30) REVERT: M 25 PHE cc_start: 0.7605 (m-10) cc_final: 0.7329 (m-10) REVERT: M 49 VAL cc_start: 0.7923 (t) cc_final: 0.7626 (p) REVERT: M 56 GLU cc_start: 0.7930 (tt0) cc_final: 0.7247 (tt0) REVERT: M 64 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8189 (tm-30) REVERT: N 43 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8163 (tptp) REVERT: N 44 VAL cc_start: 0.9053 (t) cc_final: 0.8712 (t) REVERT: O 41 TYR cc_start: 0.6460 (m-80) cc_final: 0.5894 (m-80) REVERT: O 61 LEU cc_start: 0.8590 (mt) cc_final: 0.7135 (mp) REVERT: O 64 LYS cc_start: 0.8506 (pptt) cc_final: 0.8238 (pptt) REVERT: O 65 LEU cc_start: 0.8185 (tp) cc_final: 0.7915 (tp) REVERT: O 76 GLN cc_start: 0.9077 (tt0) cc_final: 0.8655 (tp40) REVERT: O 96 CYS cc_start: 0.9427 (m) cc_final: 0.8416 (m) REVERT: O 101 VAL cc_start: 0.9430 (m) cc_final: 0.8874 (p) REVERT: O 105 GLU cc_start: 0.9247 (pt0) cc_final: 0.8932 (pt0) REVERT: P 84 MET cc_start: 0.7141 (tpp) cc_final: 0.6831 (tpp) REVERT: P 88 TYR cc_start: 0.8208 (m-80) cc_final: 0.6875 (t80) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.3182 time to fit residues: 191.1108 Evaluate side-chains 317 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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: 5.9990 chunk 118 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 24 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 M 31 HIS ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN O 125 GLN P 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.074163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.052171 restraints weight = 123861.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.053744 restraints weight = 63742.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054102 restraints weight = 36456.377| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 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 = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21551 Z= 0.239 Angle : 0.676 11.736 31255 Z= 0.391 Chirality : 0.037 0.161 3561 Planarity : 0.005 0.051 2220 Dihedral : 33.035 178.545 6852 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % 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: 1.23 (0.22), residues: 1219 helix: 1.26 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS B 75 PHE 0.024 0.002 PHE F 61 TYR 0.030 0.002 TYR E 99 ARG 0.009 0.001 ARG L 35 Details of bonding type rmsd hydrogen bonds : bond 0.06166 ( 1312) hydrogen bonds : angle 3.81415 ( 3284) covalent geometry : bond 0.00522 (21551) covalent geometry : angle 0.67550 (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 359 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8411 (m-80) cc_final: 0.8194 (m-10) REVERT: A 93 GLN cc_start: 0.8963 (tp40) cc_final: 0.8222 (tp40) REVERT: A 106 ASP cc_start: 0.9052 (m-30) cc_final: 0.8403 (m-30) REVERT: A 110 CYS cc_start: 0.9174 (m) cc_final: 0.8949 (t) REVERT: A 123 ASP cc_start: 0.8333 (m-30) cc_final: 0.7947 (m-30) REVERT: B 37 LEU cc_start: 0.9447 (mm) cc_final: 0.9216 (mm) REVERT: B 40 ARG cc_start: 0.9042 (mtp180) cc_final: 0.8658 (tpp80) REVERT: B 44 LYS cc_start: 0.7944 (tttm) cc_final: 0.7533 (tttt) REVERT: B 45 ARG cc_start: 0.7847 (tpt-90) cc_final: 0.6652 (tpt-90) REVERT: B 52 GLU cc_start: 0.8335 (mp0) cc_final: 0.8093 (mp0) REVERT: B 63 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8388 (tm-30) REVERT: B 68 ASP cc_start: 0.9102 (m-30) cc_final: 0.8869 (m-30) REVERT: B 74 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 98 TYR cc_start: 0.8791 (m-10) cc_final: 0.8371 (m-10) REVERT: C 39 TYR cc_start: 0.8786 (m-80) cc_final: 0.8167 (m-80) REVERT: C 104 GLN cc_start: 0.8382 (mt0) cc_final: 0.7801 (mm-40) REVERT: D 44 VAL cc_start: 0.9528 (t) cc_final: 0.9270 (p) REVERT: E 50 GLU cc_start: 0.8395 (mm-30) cc_final: 0.6948 (tp30) REVERT: E 54 TYR cc_start: 0.8431 (m-10) cc_final: 0.7174 (m-80) REVERT: E 94 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8236 (mt-10) REVERT: E 113 HIS cc_start: 0.8599 (t70) cc_final: 0.8051 (t-90) REVERT: F 79 LYS cc_start: 0.7285 (mmtt) cc_final: 0.6524 (mmtt) REVERT: F 88 TYR cc_start: 0.8390 (m-10) cc_final: 0.8104 (m-10) REVERT: G 38 ASN cc_start: 0.8525 (m110) cc_final: 0.8249 (t0) REVERT: G 61 GLU cc_start: 0.8600 (tp30) cc_final: 0.8288 (mm-30) REVERT: G 68 ASN cc_start: 0.9195 (m110) cc_final: 0.8769 (m-40) REVERT: G 95 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7894 (tmtt) REVERT: H 37 TYR cc_start: 0.8836 (m-80) cc_final: 0.7921 (m-10) REVERT: H 68 ASP cc_start: 0.8799 (t0) cc_final: 0.8405 (t0) REVERT: H 112 SER cc_start: 0.9323 (t) cc_final: 0.9002 (p) REVERT: K 90 MET cc_start: 0.8658 (mpp) cc_final: 0.8384 (mpp) REVERT: K 103 LEU cc_start: 0.9212 (mt) cc_final: 0.8975 (mt) REVERT: K 107 THR cc_start: 0.9158 (p) cc_final: 0.8456 (p) REVERT: K 123 ASP cc_start: 0.8622 (m-30) cc_final: 0.7952 (t0) REVERT: K 131 ARG cc_start: 0.7758 (tpp80) cc_final: 0.7354 (tpp80) REVERT: M 49 VAL cc_start: 0.7837 (t) cc_final: 0.7496 (p) REVERT: M 64 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8122 (tm-30) REVERT: N 43 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8195 (tptp) REVERT: N 44 VAL cc_start: 0.9041 (t) cc_final: 0.8800 (t) REVERT: O 41 TYR cc_start: 0.6571 (m-80) cc_final: 0.5996 (m-80) REVERT: O 65 LEU cc_start: 0.8005 (tp) cc_final: 0.7795 (tp) REVERT: O 76 GLN cc_start: 0.9038 (tt0) cc_final: 0.8471 (tp40) REVERT: O 96 CYS cc_start: 0.9439 (m) cc_final: 0.9117 (m) REVERT: O 97 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8839 (mp0) REVERT: O 99 TYR cc_start: 0.8776 (t80) cc_final: 0.8490 (t80) REVERT: O 101 VAL cc_start: 0.9491 (m) cc_final: 0.8897 (p) REVERT: O 105 GLU cc_start: 0.9247 (pt0) cc_final: 0.8922 (pt0) REVERT: P 44 LYS cc_start: 0.7315 (tttt) cc_final: 0.7040 (tptm) REVERT: P 53 GLU cc_start: 0.8388 (tt0) cc_final: 0.8186 (pt0) REVERT: P 59 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8997 (mmmm) REVERT: P 61 PHE cc_start: 0.8935 (t80) cc_final: 0.8706 (t80) REVERT: P 72 TYR cc_start: 0.7440 (m-10) cc_final: 0.7209 (m-10) outliers start: 1 outliers final: 0 residues processed: 359 average time/residue: 0.2912 time to fit residues: 161.9625 Evaluate side-chains 299 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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: 4.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN L 25 ASN P 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.074116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052326 restraints weight = 118697.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.053819 restraints weight = 58025.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.054770 restraints weight = 36633.986| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21551 Z= 0.190 Angle : 0.653 10.438 31255 Z= 0.379 Chirality : 0.036 0.169 3561 Planarity : 0.005 0.090 2220 Dihedral : 32.990 177.502 6852 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.10 % Allowed : 1.63 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.22), residues: 1219 helix: 1.24 (0.16), residues: 932 sheet: None (None), residues: 0 loop : -0.72 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS B 75 PHE 0.018 0.002 PHE B 61 TYR 0.033 0.002 TYR L 88 ARG 0.021 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05332 ( 1312) hydrogen bonds : angle 3.64985 ( 3284) covalent geometry : bond 0.00416 (21551) covalent geometry : angle 0.65260 (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 356 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8318 (m-80) cc_final: 0.8027 (m-80) REVERT: A 93 GLN cc_start: 0.8914 (tp40) cc_final: 0.8421 (tp40) REVERT: A 99 TYR cc_start: 0.8553 (t80) cc_final: 0.8348 (t80) REVERT: A 106 ASP cc_start: 0.9089 (m-30) cc_final: 0.8489 (m-30) REVERT: A 110 CYS cc_start: 0.9253 (m) cc_final: 0.8841 (t) REVERT: A 123 ASP cc_start: 0.8466 (m-30) cc_final: 0.7728 (m-30) REVERT: B 37 LEU cc_start: 0.9399 (mm) cc_final: 0.9160 (mm) REVERT: B 40 ARG cc_start: 0.8931 (mtp180) cc_final: 0.8727 (tpp80) REVERT: B 44 LYS cc_start: 0.7891 (tttm) cc_final: 0.7492 (tttt) REVERT: B 45 ARG cc_start: 0.8244 (tpt-90) cc_final: 0.7079 (tpt-90) REVERT: B 52 GLU cc_start: 0.8500 (mp0) cc_final: 0.8248 (mp0) REVERT: B 63 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8443 (tm-30) REVERT: B 68 ASP cc_start: 0.9165 (m-30) cc_final: 0.8933 (m-30) REVERT: B 74 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 98 TYR cc_start: 0.8868 (m-10) cc_final: 0.8392 (m-80) REVERT: C 39 TYR cc_start: 0.8850 (m-80) cc_final: 0.8252 (m-80) REVERT: C 104 GLN cc_start: 0.8431 (mt0) cc_final: 0.7773 (mt0) REVERT: D 44 VAL cc_start: 0.9442 (t) cc_final: 0.9156 (p) REVERT: D 100 LEU cc_start: 0.8860 (mm) cc_final: 0.8426 (mm) REVERT: E 50 GLU cc_start: 0.8287 (mm-30) cc_final: 0.6687 (tp30) REVERT: E 54 TYR cc_start: 0.8444 (m-10) cc_final: 0.7126 (m-80) REVERT: E 82 LEU cc_start: 0.8024 (pt) cc_final: 0.7800 (pt) REVERT: E 94 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8680 (mt-10) REVERT: E 109 LEU cc_start: 0.9202 (mp) cc_final: 0.8545 (mt) REVERT: E 112 ILE cc_start: 0.8983 (mm) cc_final: 0.8772 (pt) REVERT: E 113 HIS cc_start: 0.8265 (t70) cc_final: 0.7708 (t70) REVERT: F 44 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8207 (mtpp) REVERT: F 79 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6610 (mmtt) REVERT: G 38 ASN cc_start: 0.8837 (m110) cc_final: 0.8509 (t0) REVERT: G 61 GLU cc_start: 0.8716 (tp30) cc_final: 0.8495 (mm-30) REVERT: G 68 ASN cc_start: 0.9195 (m110) cc_final: 0.8816 (t0) REVERT: G 95 LYS cc_start: 0.8377 (ttmt) cc_final: 0.7902 (tmtt) REVERT: H 37 TYR cc_start: 0.8884 (m-80) cc_final: 0.7878 (m-10) REVERT: H 68 ASP cc_start: 0.8719 (t0) cc_final: 0.8490 (t0) REVERT: H 95 GLN cc_start: 0.9108 (tt0) cc_final: 0.7965 (tm-30) REVERT: H 112 SER cc_start: 0.9271 (t) cc_final: 0.8961 (p) REVERT: K 65 LEU cc_start: 0.7717 (tp) cc_final: 0.7499 (tt) REVERT: K 90 MET cc_start: 0.8830 (mpp) cc_final: 0.8550 (mpp) REVERT: K 103 LEU cc_start: 0.9259 (mt) cc_final: 0.8994 (mt) REVERT: K 131 ARG cc_start: 0.7754 (tpp80) cc_final: 0.7390 (tpp80) REVERT: M 25 PHE cc_start: 0.6436 (m-10) cc_final: 0.6113 (m-10) REVERT: M 61 GLU cc_start: 0.9255 (pt0) cc_final: 0.9027 (pt0) REVERT: M 64 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8174 (tm-30) REVERT: N 43 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8196 (tptp) REVERT: O 41 TYR cc_start: 0.6888 (m-80) cc_final: 0.6298 (m-80) REVERT: O 61 LEU cc_start: 0.7730 (mt) cc_final: 0.7127 (mp) REVERT: O 76 GLN cc_start: 0.9023 (tt0) cc_final: 0.8481 (tp40) REVERT: O 90 MET cc_start: 0.9168 (ptp) cc_final: 0.8961 (ptm) REVERT: O 96 CYS cc_start: 0.9415 (m) cc_final: 0.8472 (m) REVERT: O 99 TYR cc_start: 0.8773 (t80) cc_final: 0.8432 (t80) REVERT: O 101 VAL cc_start: 0.9477 (m) cc_final: 0.8904 (p) REVERT: O 105 GLU cc_start: 0.9258 (pt0) cc_final: 0.8941 (pt0) REVERT: P 44 LYS cc_start: 0.7233 (tttt) cc_final: 0.7008 (tptm) REVERT: P 59 LYS cc_start: 0.9242 (mmmm) cc_final: 0.9023 (mmmm) REVERT: P 61 PHE cc_start: 0.8946 (t80) cc_final: 0.8702 (t80) REVERT: P 84 MET cc_start: 0.7200 (tpp) cc_final: 0.6501 (tpp) REVERT: P 88 TYR cc_start: 0.8415 (m-80) cc_final: 0.7118 (t80) REVERT: P 98 TYR cc_start: 0.6763 (m-80) cc_final: 0.6548 (m-80) outliers start: 1 outliers final: 0 residues processed: 356 average time/residue: 0.2840 time to fit residues: 156.9260 Evaluate side-chains 296 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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: 5.9990 chunk 8 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 152 optimal weight: 30.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.075457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.053488 restraints weight = 118213.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.054998 restraints weight = 57960.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.055961 restraints weight = 36597.456| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 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 = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21551 Z= 0.161 Angle : 0.640 7.960 31255 Z= 0.370 Chirality : 0.036 0.180 3561 Planarity : 0.005 0.072 2220 Dihedral : 32.783 178.076 6852 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 1.33 (0.23), residues: 1219 helix: 1.37 (0.16), residues: 935 sheet: None (None), residues: 0 loop : -0.61 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 75 PHE 0.026 0.002 PHE D 65 TYR 0.026 0.002 TYR P 98 ARG 0.011 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 1312) hydrogen bonds : angle 3.50785 ( 3284) covalent geometry : bond 0.00348 (21551) covalent geometry : angle 0.63969 (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 364 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.487 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: A 84 PHE cc_start: 0.8090 (m-80) cc_final: 0.7866 (m-10) REVERT: A 93 GLN cc_start: 0.8765 (tp40) cc_final: 0.8218 (tp40) REVERT: A 106 ASP cc_start: 0.9120 (m-30) cc_final: 0.8631 (m-30) REVERT: A 110 CYS cc_start: 0.9312 (m) cc_final: 0.8851 (t) REVERT: A 123 ASP cc_start: 0.8424 (m-30) cc_final: 0.7590 (m-30) REVERT: B 40 ARG cc_start: 0.8899 (mtp180) cc_final: 0.8485 (tpp80) REVERT: B 52 GLU cc_start: 0.8586 (mp0) cc_final: 0.8361 (mp0) REVERT: B 63 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8357 (tm-30) REVERT: B 67 ARG cc_start: 0.8822 (tpp80) cc_final: 0.8393 (tpp80) REVERT: B 68 ASP cc_start: 0.9207 (m-30) cc_final: 0.8902 (m-30) REVERT: B 74 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 98 TYR cc_start: 0.8892 (m-10) cc_final: 0.8241 (m-10) REVERT: C 39 TYR cc_start: 0.8730 (m-80) cc_final: 0.7966 (m-80) REVERT: C 104 GLN cc_start: 0.8336 (mt0) cc_final: 0.7802 (mt0) REVERT: D 62 MET cc_start: 0.8588 (mmm) cc_final: 0.8328 (mmp) REVERT: D 68 ASP cc_start: 0.8398 (t70) cc_final: 0.8101 (t0) REVERT: D 100 LEU cc_start: 0.8927 (mm) cc_final: 0.8545 (mm) REVERT: E 50 GLU cc_start: 0.8355 (mm-30) cc_final: 0.6602 (tp30) REVERT: E 54 TYR cc_start: 0.8352 (m-10) cc_final: 0.7019 (m-80) REVERT: E 67 PHE cc_start: 0.8165 (t80) cc_final: 0.7895 (t80) REVERT: E 82 LEU cc_start: 0.7976 (pt) cc_final: 0.7726 (pt) REVERT: E 90 MET cc_start: 0.8731 (tpp) cc_final: 0.8265 (mmm) REVERT: E 93 GLN cc_start: 0.8515 (tt0) cc_final: 0.7464 (tt0) REVERT: E 113 HIS cc_start: 0.8353 (t70) cc_final: 0.7753 (t70) REVERT: F 27 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8256 (mp10) REVERT: F 44 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8214 (mtpp) REVERT: F 79 LYS cc_start: 0.7295 (mmtt) cc_final: 0.6530 (mmtt) REVERT: F 98 TYR cc_start: 0.9104 (m-10) cc_final: 0.8812 (m-10) REVERT: G 38 ASN cc_start: 0.8686 (m110) cc_final: 0.8457 (t0) REVERT: G 68 ASN cc_start: 0.9072 (m110) cc_final: 0.8779 (t0) REVERT: G 95 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7961 (tmtt) REVERT: H 37 TYR cc_start: 0.8845 (m-80) cc_final: 0.8048 (m-10) REVERT: H 68 ASP cc_start: 0.8589 (t0) cc_final: 0.8121 (t0) REVERT: H 112 SER cc_start: 0.8959 (t) cc_final: 0.8672 (p) REVERT: H 113 GLU cc_start: 0.8424 (mp0) cc_final: 0.8075 (mp0) REVERT: K 65 LEU cc_start: 0.7826 (tp) cc_final: 0.7584 (tt) REVERT: K 103 LEU cc_start: 0.9240 (mt) cc_final: 0.8969 (mt) REVERT: K 107 THR cc_start: 0.9111 (p) cc_final: 0.8338 (p) REVERT: K 123 ASP cc_start: 0.8658 (m-30) cc_final: 0.7817 (t0) REVERT: K 131 ARG cc_start: 0.7646 (tpp80) cc_final: 0.7373 (tpp80) REVERT: M 25 PHE cc_start: 0.6492 (m-10) cc_final: 0.6115 (m-10) REVERT: M 56 GLU cc_start: 0.7930 (tt0) cc_final: 0.7472 (mt-10) REVERT: M 61 GLU cc_start: 0.9240 (pt0) cc_final: 0.9006 (pt0) REVERT: M 64 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8190 (tm-30) REVERT: M 91 GLU cc_start: 0.8306 (pm20) cc_final: 0.8045 (pm20) REVERT: N 43 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8154 (tptp) REVERT: N 45 LEU cc_start: 0.9082 (tt) cc_final: 0.8859 (tt) REVERT: O 76 GLN cc_start: 0.9026 (tt0) cc_final: 0.8598 (tp40) REVERT: O 96 CYS cc_start: 0.9372 (m) cc_final: 0.8448 (m) REVERT: O 99 TYR cc_start: 0.8739 (t80) cc_final: 0.8447 (t80) REVERT: O 101 VAL cc_start: 0.9488 (m) cc_final: 0.8925 (p) REVERT: O 105 GLU cc_start: 0.9297 (pt0) cc_final: 0.8974 (pt0) REVERT: P 44 LYS cc_start: 0.7318 (tttt) cc_final: 0.7084 (tptm) REVERT: P 59 LYS cc_start: 0.9282 (mmmm) cc_final: 0.9073 (mmmm) REVERT: P 72 TYR cc_start: 0.7988 (m-80) cc_final: 0.7690 (m-10) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3016 time to fit residues: 169.3256 Evaluate side-chains 288 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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: 10.0000 chunk 92 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 0.0030 chunk 58 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 overall best weight: 5.0002 ------------------------------------------------------------------------------- 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 31 HIS C 110 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.072715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.051216 restraints weight = 124481.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.052441 restraints weight = 63762.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053051 restraints weight = 37727.785| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21551 Z= 0.260 Angle : 0.728 12.871 31255 Z= 0.414 Chirality : 0.039 0.372 3561 Planarity : 0.006 0.067 2220 Dihedral : 33.307 178.920 6852 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 0.78 (0.22), residues: 1219 helix: 0.94 (0.16), residues: 939 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 75 PHE 0.040 0.003 PHE P 61 TYR 0.064 0.004 TYR N 42 ARG 0.012 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.06647 ( 1312) hydrogen bonds : angle 4.04459 ( 3284) covalent geometry : bond 0.00568 (21551) covalent geometry : angle 0.72792 (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 326 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.418 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: A 84 PHE cc_start: 0.8405 (m-80) cc_final: 0.8189 (m-10) REVERT: A 93 GLN cc_start: 0.8783 (tp40) cc_final: 0.8308 (tp40) REVERT: A 105 GLU cc_start: 0.7110 (pp20) cc_final: 0.6670 (pp20) REVERT: A 106 ASP cc_start: 0.8729 (m-30) cc_final: 0.8289 (m-30) REVERT: A 120 MET cc_start: 0.9122 (mtm) cc_final: 0.8917 (mtp) REVERT: B 44 LYS cc_start: 0.8087 (tttm) cc_final: 0.7632 (tttt) REVERT: B 45 ARG cc_start: 0.8262 (tpt-90) cc_final: 0.7886 (tpt-90) REVERT: B 52 GLU cc_start: 0.8620 (mp0) cc_final: 0.8409 (mp0) REVERT: B 63 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8446 (tm-30) REVERT: B 74 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 98 TYR cc_start: 0.8807 (m-10) cc_final: 0.8562 (m-80) REVERT: C 39 TYR cc_start: 0.8768 (m-80) cc_final: 0.8232 (m-80) REVERT: C 57 TYR cc_start: 0.8760 (t80) cc_final: 0.8546 (t80) REVERT: C 104 GLN cc_start: 0.8328 (mt0) cc_final: 0.8067 (mt0) REVERT: D 42 TYR cc_start: 0.8756 (t80) cc_final: 0.8513 (t80) REVERT: D 59 MET cc_start: 0.8981 (tpp) cc_final: 0.8721 (tpp) REVERT: D 68 ASP cc_start: 0.8379 (t70) cc_final: 0.8018 (t0) REVERT: E 50 GLU cc_start: 0.8219 (mm-30) cc_final: 0.6547 (tp30) REVERT: E 54 TYR cc_start: 0.8428 (m-10) cc_final: 0.7144 (m-80) REVERT: E 67 PHE cc_start: 0.8258 (t80) cc_final: 0.7937 (t80) REVERT: E 82 LEU cc_start: 0.7976 (pt) cc_final: 0.7776 (pt) REVERT: E 113 HIS cc_start: 0.8251 (t70) cc_final: 0.7518 (t70) REVERT: F 79 LYS cc_start: 0.7400 (mmtt) cc_final: 0.6651 (mmtt) REVERT: F 88 TYR cc_start: 0.8613 (m-10) cc_final: 0.8249 (m-80) REVERT: G 38 ASN cc_start: 0.8837 (m110) cc_final: 0.8486 (t0) REVERT: G 68 ASN cc_start: 0.9146 (m110) cc_final: 0.8696 (t0) REVERT: G 95 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7950 (tmtt) REVERT: H 37 TYR cc_start: 0.8871 (m-80) cc_final: 0.7874 (m-10) REVERT: H 112 SER cc_start: 0.9054 (t) cc_final: 0.8628 (p) REVERT: K 90 MET cc_start: 0.8681 (mmp) cc_final: 0.8411 (mmp) REVERT: K 103 LEU cc_start: 0.9160 (mt) cc_final: 0.8928 (mt) REVERT: K 120 MET cc_start: 0.5845 (mtp) cc_final: 0.5572 (mtp) REVERT: K 131 ARG cc_start: 0.7740 (tpp80) cc_final: 0.7371 (tpp80) REVERT: M 25 PHE cc_start: 0.6407 (m-10) cc_final: 0.6016 (m-10) REVERT: M 61 GLU cc_start: 0.9185 (pt0) cc_final: 0.8870 (pt0) REVERT: M 64 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8140 (tm-30) REVERT: M 68 ASN cc_start: 0.9073 (m110) cc_final: 0.8790 (m110) REVERT: N 43 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8231 (tptp) REVERT: N 102 LEU cc_start: 0.7997 (mm) cc_final: 0.7762 (tp) REVERT: O 64 LYS cc_start: 0.8301 (pptt) cc_final: 0.8039 (pptt) REVERT: O 65 LEU cc_start: 0.8091 (tp) cc_final: 0.7665 (tp) REVERT: O 76 GLN cc_start: 0.8697 (tt0) cc_final: 0.8201 (tp40) REVERT: O 84 PHE cc_start: 0.6480 (m-80) cc_final: 0.5096 (p90) REVERT: O 96 CYS cc_start: 0.9385 (m) cc_final: 0.8929 (m) REVERT: O 101 VAL cc_start: 0.9571 (m) cc_final: 0.9036 (p) REVERT: O 105 GLU cc_start: 0.9292 (pt0) cc_final: 0.8985 (pt0) REVERT: P 44 LYS cc_start: 0.7404 (tttt) cc_final: 0.7180 (tptm) REVERT: P 59 LYS cc_start: 0.9256 (mmmm) cc_final: 0.8993 (mmmm) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2895 time to fit residues: 147.3482 Evaluate side-chains 264 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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: 8.9990 chunk 78 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 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** P 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.070849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048291 restraints weight = 127924.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.049708 restraints weight = 66555.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050046 restraints weight = 38579.991| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.7756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 21551 Z= 0.338 Angle : 0.806 13.174 31255 Z= 0.463 Chirality : 0.043 0.183 3561 Planarity : 0.007 0.065 2220 Dihedral : 33.953 179.671 6852 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -0.09 (0.22), residues: 1219 helix: 0.36 (0.16), residues: 933 sheet: None (None), residues: 0 loop : -1.13 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS B 75 PHE 0.020 0.003 PHE P 61 TYR 0.035 0.003 TYR P 72 ARG 0.012 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.08668 ( 1312) hydrogen bonds : angle 4.53956 ( 3284) covalent geometry : bond 0.00736 (21551) covalent geometry : angle 0.80593 (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 317 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8810 (pm20) cc_final: 0.8536 (pm20) REVERT: A 84 PHE cc_start: 0.8533 (m-80) cc_final: 0.8290 (m-10) REVERT: A 93 GLN cc_start: 0.8857 (tp40) cc_final: 0.8471 (tp40) REVERT: A 105 GLU cc_start: 0.7649 (pp20) cc_final: 0.7227 (pp20) REVERT: A 106 ASP cc_start: 0.8741 (m-30) cc_final: 0.8279 (m-30) REVERT: A 120 MET cc_start: 0.9110 (mtm) cc_final: 0.8885 (mtp) REVERT: B 44 LYS cc_start: 0.8054 (tttm) cc_final: 0.7559 (tttt) REVERT: B 45 ARG cc_start: 0.8260 (tpt-90) cc_final: 0.7910 (tpt-90) REVERT: B 52 GLU cc_start: 0.8649 (mp0) cc_final: 0.8415 (mp0) REVERT: B 63 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8398 (tm-30) REVERT: B 67 ARG cc_start: 0.8969 (tpp80) cc_final: 0.8687 (tpp80) REVERT: B 74 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 39 TYR cc_start: 0.8745 (m-80) cc_final: 0.8297 (m-80) REVERT: D 62 MET cc_start: 0.8485 (mmm) cc_final: 0.8221 (mmp) REVERT: D 68 ASP cc_start: 0.8429 (t70) cc_final: 0.8168 (t0) REVERT: E 50 GLU cc_start: 0.8117 (mm-30) cc_final: 0.6247 (tp30) REVERT: E 54 TYR cc_start: 0.8481 (m-10) cc_final: 0.7273 (m-80) REVERT: E 90 MET cc_start: 0.8791 (tpp) cc_final: 0.8028 (tpp) REVERT: E 93 GLN cc_start: 0.8254 (tt0) cc_final: 0.7385 (tt0) REVERT: E 94 GLU cc_start: 0.8792 (tt0) cc_final: 0.8551 (tt0) REVERT: E 103 LEU cc_start: 0.9367 (tt) cc_final: 0.9065 (tt) REVERT: F 27 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8662 (mm-40) REVERT: F 44 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8328 (mtpt) REVERT: F 79 LYS cc_start: 0.7426 (mmtt) cc_final: 0.6972 (mmtt) REVERT: F 88 TYR cc_start: 0.8665 (m-10) cc_final: 0.8258 (m-80) REVERT: G 38 ASN cc_start: 0.8949 (m110) cc_final: 0.8637 (t0) REVERT: G 56 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8143 (tp30) REVERT: G 68 ASN cc_start: 0.9146 (m110) cc_final: 0.8624 (t0) REVERT: G 95 LYS cc_start: 0.8526 (ttmt) cc_final: 0.7931 (tmtt) REVERT: H 37 TYR cc_start: 0.8918 (m-80) cc_final: 0.8031 (m-10) REVERT: H 112 SER cc_start: 0.9259 (t) cc_final: 0.8886 (p) REVERT: H 113 GLU cc_start: 0.8618 (mp0) cc_final: 0.8258 (mp0) REVERT: K 90 MET cc_start: 0.8804 (mmp) cc_final: 0.8443 (mmp) REVERT: K 120 MET cc_start: 0.5968 (mtp) cc_final: 0.5709 (mtp) REVERT: K 131 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7450 (tpp80) REVERT: M 61 GLU cc_start: 0.9175 (pt0) cc_final: 0.8863 (pt0) REVERT: M 64 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8153 (tm-30) REVERT: M 68 ASN cc_start: 0.9139 (m110) cc_final: 0.8795 (m-40) REVERT: N 43 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8388 (tptp) REVERT: N 80 LEU cc_start: 0.8097 (mt) cc_final: 0.7739 (mt) REVERT: O 61 LEU cc_start: 0.7049 (mt) cc_final: 0.6544 (mp) REVERT: O 67 PHE cc_start: 0.8766 (t80) cc_final: 0.8471 (t80) REVERT: O 92 LEU cc_start: 0.9446 (mm) cc_final: 0.9152 (mm) REVERT: O 96 CYS cc_start: 0.9232 (m) cc_final: 0.8788 (m) REVERT: O 101 VAL cc_start: 0.9560 (m) cc_final: 0.8930 (p) REVERT: O 105 GLU cc_start: 0.9310 (pt0) cc_final: 0.8983 (pt0) REVERT: O 125 GLN cc_start: 0.9465 (mp10) cc_final: 0.9229 (mm-40) REVERT: P 44 LYS cc_start: 0.7308 (tttt) cc_final: 0.7066 (tptm) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2747 time to fit residues: 137.4542 Evaluate side-chains 260 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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: 4.9990 chunk 85 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.073536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050805 restraints weight = 129770.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051992 restraints weight = 73670.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.052305 restraints weight = 47334.574| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.7762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21551 Z= 0.217 Angle : 0.720 9.955 31255 Z= 0.413 Chirality : 0.039 0.200 3561 Planarity : 0.005 0.062 2220 Dihedral : 33.748 178.343 6852 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 0.27 (0.22), residues: 1219 helix: 0.64 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -1.11 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS B 75 PHE 0.024 0.003 PHE F 61 TYR 0.049 0.003 TYR B 88 ARG 0.013 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.06084 ( 1312) hydrogen bonds : angle 4.07624 ( 3284) covalent geometry : bond 0.00477 (21551) covalent geometry : angle 0.71989 (31255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6556.29 seconds wall clock time: 114 minutes 34.71 seconds (6874.71 seconds total)