Starting phenix.real_space_refine on Sun Aug 24 05:24:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u13_41800/08_2025/8u13_41800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u13_41800/08_2025/8u13_41800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u13_41800/08_2025/8u13_41800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u13_41800/08_2025/8u13_41800.map" model { file = "/net/cci-nas-00/data/ceres_data/8u13_41800/08_2025/8u13_41800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u13_41800/08_2025/8u13_41800.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 293 5.49 5 S 25 5.16 5 C 7139 2.51 5 N 2408 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12825 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 735 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 706 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Conformer: "B" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} bond proxies already assigned to first conformer: 713 Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 843 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10617 SG CYS K 31 27.021 59.998 74.288 1.00394.38 S ATOM 10767 SG CYS K 51 26.391 63.713 73.415 1.00417.10 S ATOM 10791 SG CYS K 54 27.019 62.691 77.048 1.00421.64 S ATOM 10508 SG CYS K 16 19.411 66.329 66.379 1.00424.33 S ATOM 10526 SG CYS K 19 18.344 69.167 64.157 1.00433.92 S ATOM 10656 SG CYS K 36 20.356 66.435 62.624 1.00418.58 S ATOM 10678 SG CYS K 39 21.999 68.761 65.379 1.00418.47 S Time building chain proxies: 3.22, per 1000 atoms: 0.25 Number of scatterers: 12825 At special positions: 0 Unit cell: (103.788, 117.146, 117.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 25 16.00 P 293 15.00 O 2958 8.00 N 2408 7.00 C 7139 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 518.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " Number of angles added : 9 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 68.9% alpha, 2.6% beta 141 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.756A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.685A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.498A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.528A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) 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 56 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.657A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.933A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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 removed outlier: 3.654A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 36 through 45 Processing helix chain 'K' and resid 58 through 68 removed outlier: 4.417A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 removed outlier: 4.140A pdb=" N ARG K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.543A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.449A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.391A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.545A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.565A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.296A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.579A pdb=" N VAL K 27 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 432 hydrogen bonds defined for protein. 1273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 359 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.62 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: 2525 1.33 - 1.45: 4369 1.45 - 1.57: 6137 1.57 - 1.69: 584 1.69 - 1.81: 36 Bond restraints: 13651 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CG GLU B 63 " pdb=" CD GLU B 63 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.05e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.80e+00 bond pdb=" CB ARG F 39 " pdb=" CG ARG F 39 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CG1 ILE G 62 " pdb=" CD1 ILE G 62 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.17e+00 ... (remaining 13646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 19055 1.60 - 3.20: 559 3.20 - 4.79: 49 4.79 - 6.39: 22 6.39 - 7.99: 7 Bond angle restraints: 19692 Sorted by residual: angle pdb=" N GLU B 63 " pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " ideal model delta sigma weight residual 110.28 116.80 -6.52 1.55e+00 4.16e-01 1.77e+01 angle pdb=" C LEU B 62 " pdb=" N GLU B 63 " pdb=" CA GLU B 63 " ideal model delta sigma weight residual 120.31 114.63 5.68 1.52e+00 4.33e-01 1.40e+01 angle pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " pdb=" CG GLU B 63 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 angle pdb=" C SER H 112 " pdb=" N GLU H 113 " pdb=" CA GLU H 113 " ideal model delta sigma weight residual 121.14 115.58 5.56 1.75e+00 3.27e-01 1.01e+01 angle pdb=" C GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 109.72 115.15 -5.43 1.92e+00 2.71e-01 8.00e+00 ... (remaining 19687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.48: 6095 34.48 - 68.96: 1363 68.96 - 103.44: 29 103.44 - 137.92: 0 137.92 - 172.40: 2 Dihedral angle restraints: 7489 sinusoidal: 4990 harmonic: 2499 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 47.60 172.40 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1866 0.045 - 0.091: 309 0.091 - 0.136: 61 0.136 - 0.181: 4 0.181 - 0.226: 1 Chirality restraints: 2241 Sorted by residual: chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE E 51 " pdb=" CA ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CG2 ILE E 51 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA TYR E 54 " pdb=" N TYR E 54 " pdb=" C TYR E 54 " pdb=" CB TYR E 54 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 2238 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 129 " 0.169 9.50e-02 1.11e+02 7.58e-02 3.72e+00 pdb=" NE ARG E 129 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 129 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 129 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 129 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 113 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" CD GLU H 113 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU H 113 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU H 113 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 48 " 0.022 2.00e-02 2.50e+03 9.15e-03 2.51e+00 pdb=" N9 DG I 48 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I 48 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DG I 48 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 48 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 48 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 48 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 48 " -0.002 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 483 2.70 - 3.25: 12231 3.25 - 3.80: 25255 3.80 - 4.35: 30112 4.35 - 4.90: 42904 Nonbonded interactions: 110985 Sorted by model distance: nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.145 3.120 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.153 2.496 nonbonded pdb=" OE1 GLU D 71 " pdb=" OH TYR C 39 " model vdw 2.180 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.240 3.040 nonbonded pdb=" NH2 ARG E 42 " pdb=" OP1 DG J -5 " model vdw 2.249 3.120 ... (remaining 110980 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' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 119) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 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=0.00 max=1.00 mean=1.00 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.540 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 0.045 13661 Z= 0.163 Angle : 0.641 7.991 19707 Z= 0.368 Chirality : 0.036 0.226 2241 Planarity : 0.005 0.076 1475 Dihedral : 27.097 172.397 5871 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.28), residues: 842 helix: 1.16 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.84 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 99 TYR 0.021 0.002 TYR B 88 PHE 0.009 0.001 PHE G 25 TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00351 (13651) covalent geometry : angle 0.63756 (19692) hydrogen bonds : bond 0.10747 ( 791) hydrogen bonds : angle 4.26585 ( 1987) metal coordination : bond 0.00645 ( 8) metal coordination : angle 3.29907 ( 9) link_TRANS : bond 0.00262 ( 2) link_TRANS : angle 0.86790 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7092 (mt-10) REVERT: A 125 GLN cc_start: 0.9259 (mp10) cc_final: 0.8940 (mp10) REVERT: B 23 ARG cc_start: 0.8496 (mmp80) cc_final: 0.8126 (mmp80) REVERT: B 25 ASN cc_start: 0.8800 (m110) cc_final: 0.8440 (m110) REVERT: B 49 LEU cc_start: 0.9349 (pt) cc_final: 0.8356 (pt) REVERT: B 50 ILE cc_start: 0.9347 (tp) cc_final: 0.9047 (tp) REVERT: B 88 TYR cc_start: 0.8364 (m-80) cc_final: 0.8101 (m-80) REVERT: D 34 LYS cc_start: 0.8971 (mptt) cc_final: 0.8688 (mmtm) REVERT: D 57 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8600 (mmmm) REVERT: D 105 GLU cc_start: 0.8261 (tp30) cc_final: 0.7678 (tp30) REVERT: D 109 HIS cc_start: 0.8834 (m170) cc_final: 0.8628 (m170) REVERT: D 120 LYS cc_start: 0.9231 (tttp) cc_final: 0.8842 (ttmm) REVERT: E 53 ARG cc_start: 0.8788 (tmt-80) cc_final: 0.8330 (tmt-80) REVERT: E 54 TYR cc_start: 0.7863 (m-80) cc_final: 0.7639 (m-80) REVERT: E 57 SER cc_start: 0.7526 (p) cc_final: 0.6916 (p) REVERT: E 59 GLU cc_start: 0.8178 (pm20) cc_final: 0.7882 (pm20) REVERT: E 60 LEU cc_start: 0.8664 (mm) cc_final: 0.8015 (mm) REVERT: E 68 GLN cc_start: 0.8675 (pp30) cc_final: 0.8321 (pp30) REVERT: E 81 ASP cc_start: 0.8075 (m-30) cc_final: 0.7859 (m-30) REVERT: E 92 LEU cc_start: 0.9668 (mt) cc_final: 0.9462 (mt) REVERT: E 120 MET cc_start: 0.7832 (mtt) cc_final: 0.7405 (mtp) REVERT: E 125 GLN cc_start: 0.8554 (mp10) cc_final: 0.8001 (mp10) REVERT: F 49 LEU cc_start: 0.8913 (mm) cc_final: 0.8215 (mm) REVERT: H 68 ASP cc_start: 0.8399 (t70) cc_final: 0.8061 (t0) REVERT: H 83 TYR cc_start: 0.8409 (m-10) cc_final: 0.7681 (m-10) REVERT: C 84 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8811 (tp-100) REVERT: G 61 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7763 (mm-30) REVERT: G 68 ASN cc_start: 0.8959 (m-40) cc_final: 0.8649 (m-40) REVERT: G 104 GLN cc_start: 0.8967 (mp10) cc_final: 0.8679 (mp10) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1426 time to fit residues: 67.1898 Evaluate side-chains 289 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 93 GLN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN H 82 HIS H 84 ASN C 84 GLN C 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.076085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.051952 restraints weight = 64437.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053479 restraints weight = 29762.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.054451 restraints weight = 19632.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.055030 restraints weight = 15760.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.055273 restraints weight = 14068.208| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13661 Z= 0.206 Angle : 0.660 7.942 19707 Z= 0.374 Chirality : 0.037 0.161 2241 Planarity : 0.005 0.037 1475 Dihedral : 30.140 173.015 4161 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.30 % Allowed : 17.06 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.28), residues: 842 helix: 1.22 (0.21), residues: 587 sheet: None (None), residues: 0 loop : -1.08 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 99 TYR 0.020 0.002 TYR G 57 PHE 0.019 0.002 PHE H 65 TRP 0.008 0.001 TRP K 77 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00463 (13651) covalent geometry : angle 0.65352 (19692) hydrogen bonds : bond 0.04960 ( 791) hydrogen bonds : angle 3.70783 ( 1987) metal coordination : bond 0.00751 ( 8) metal coordination : angle 4.29280 ( 9) link_TRANS : bond 0.00096 ( 2) link_TRANS : angle 0.23026 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 300 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7925 (mt-10) cc_final: 0.6983 (mt-10) REVERT: A 125 GLN cc_start: 0.9436 (mp10) cc_final: 0.8943 (mp10) REVERT: B 23 ARG cc_start: 0.8628 (mmp80) cc_final: 0.8227 (mmp80) REVERT: B 25 ASN cc_start: 0.8881 (m110) cc_final: 0.8191 (m110) REVERT: B 63 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: B 88 TYR cc_start: 0.8759 (m-10) cc_final: 0.8411 (m-80) REVERT: D 31 ARG cc_start: 0.8217 (mmp80) cc_final: 0.7885 (mmp80) REVERT: D 34 LYS cc_start: 0.8977 (mptt) cc_final: 0.8725 (mmtm) REVERT: D 57 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8629 (mmmm) REVERT: D 79 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7846 (mtm110) REVERT: D 105 GLU cc_start: 0.8482 (tp30) cc_final: 0.7100 (tp30) REVERT: D 109 HIS cc_start: 0.9156 (m170) cc_final: 0.8835 (m170) REVERT: D 120 LYS cc_start: 0.9261 (tttp) cc_final: 0.8870 (ttmm) REVERT: E 60 LEU cc_start: 0.8888 (mm) cc_final: 0.8331 (mm) REVERT: E 68 GLN cc_start: 0.8886 (pp30) cc_final: 0.8561 (pp30) REVERT: E 81 ASP cc_start: 0.8194 (m-30) cc_final: 0.7946 (m-30) REVERT: E 97 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8063 (mt-10) REVERT: F 88 TYR cc_start: 0.8690 (m-10) cc_final: 0.7623 (m-10) REVERT: H 68 ASP cc_start: 0.9103 (t70) cc_final: 0.8707 (t0) REVERT: H 83 TYR cc_start: 0.8455 (m-10) cc_final: 0.7664 (m-10) REVERT: H 86 ARG cc_start: 0.9061 (tpp80) cc_final: 0.8790 (tpp80) REVERT: C 24 GLN cc_start: 0.8548 (pm20) cc_final: 0.8270 (pm20) REVERT: C 78 ILE cc_start: 0.8952 (mm) cc_final: 0.8703 (mm) REVERT: C 84 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.8840 (tp-100) REVERT: C 91 GLU cc_start: 0.9236 (tp30) cc_final: 0.8872 (tp30) REVERT: C 92 GLU cc_start: 0.8821 (mt-10) cc_final: 0.7999 (mp0) REVERT: G 104 GLN cc_start: 0.9193 (mp10) cc_final: 0.8733 (mp10) outliers start: 24 outliers final: 12 residues processed: 307 average time/residue: 0.1414 time to fit residues: 59.0609 Evaluate side-chains 293 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 278 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 82 optimal weight: 40.0000 chunk 16 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN C 73 ASN C 89 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.074065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050339 restraints weight = 83021.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051785 restraints weight = 34314.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.052826 restraints weight = 21182.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.053428 restraints weight = 16406.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053631 restraints weight = 14365.324| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13661 Z= 0.252 Angle : 0.667 9.355 19707 Z= 0.379 Chirality : 0.038 0.174 2241 Planarity : 0.005 0.035 1475 Dihedral : 30.247 173.951 4161 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.68 % Allowed : 20.22 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.29), residues: 842 helix: 1.22 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.14 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 99 TYR 0.023 0.002 TYR G 57 PHE 0.028 0.002 PHE E 67 TRP 0.007 0.001 TRP K 61 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00566 (13651) covalent geometry : angle 0.65988 (19692) hydrogen bonds : bond 0.05285 ( 791) hydrogen bonds : angle 3.74390 ( 1987) metal coordination : bond 0.00819 ( 8) metal coordination : angle 4.65719 ( 9) link_TRANS : bond 0.00128 ( 2) link_TRANS : angle 0.32584 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7065 (mp0) REVERT: A 93 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8202 (tp40) REVERT: A 125 GLN cc_start: 0.9376 (mp10) cc_final: 0.8849 (mp10) REVERT: B 23 ARG cc_start: 0.8672 (mmp80) cc_final: 0.8253 (mmp80) REVERT: B 25 ASN cc_start: 0.8867 (m110) cc_final: 0.8290 (m110) REVERT: B 63 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: B 84 MET cc_start: 0.8637 (mmm) cc_final: 0.8351 (tpp) REVERT: B 88 TYR cc_start: 0.8862 (m-10) cc_final: 0.8542 (m-80) REVERT: D 34 LYS cc_start: 0.9039 (mptt) cc_final: 0.8739 (mmtm) REVERT: D 57 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8676 (mmmm) REVERT: D 76 GLU cc_start: 0.9293 (tp30) cc_final: 0.9045 (tp30) REVERT: D 79 ARG cc_start: 0.8354 (mtm110) cc_final: 0.7766 (mtm110) REVERT: D 105 GLU cc_start: 0.8519 (tp30) cc_final: 0.7330 (tp30) REVERT: D 120 LYS cc_start: 0.9272 (tttp) cc_final: 0.8893 (ttmm) REVERT: E 60 LEU cc_start: 0.8861 (mm) cc_final: 0.8441 (mm) REVERT: E 68 GLN cc_start: 0.8948 (pp30) cc_final: 0.8591 (pp30) REVERT: E 81 ASP cc_start: 0.8240 (m-30) cc_final: 0.7973 (m-30) REVERT: E 97 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8211 (mt-10) REVERT: E 120 MET cc_start: 0.8095 (mtt) cc_final: 0.7363 (mtp) REVERT: F 88 TYR cc_start: 0.8684 (m-10) cc_final: 0.7637 (m-10) REVERT: H 68 ASP cc_start: 0.9049 (t70) cc_final: 0.8697 (t0) REVERT: H 83 TYR cc_start: 0.8442 (m-10) cc_final: 0.7465 (m-10) REVERT: H 86 ARG cc_start: 0.9077 (tpp80) cc_final: 0.8848 (tpp80) REVERT: C 24 GLN cc_start: 0.8690 (pm20) cc_final: 0.8331 (pm20) REVERT: C 78 ILE cc_start: 0.8997 (mm) cc_final: 0.8752 (mm) REVERT: C 91 GLU cc_start: 0.9296 (tp30) cc_final: 0.8931 (tp30) REVERT: C 92 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8028 (mp0) REVERT: G 90 ASP cc_start: 0.8780 (t0) cc_final: 0.8198 (t0) REVERT: G 104 GLN cc_start: 0.9208 (mp10) cc_final: 0.8732 (mp10) outliers start: 34 outliers final: 18 residues processed: 298 average time/residue: 0.1406 time to fit residues: 56.7582 Evaluate side-chains 286 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN C 73 ASN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.074342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.049769 restraints weight = 79473.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.051413 restraints weight = 33924.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.052433 restraints weight = 21584.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.052768 restraints weight = 17028.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.053258 restraints weight = 15538.796| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13661 Z= 0.237 Angle : 0.661 8.720 19707 Z= 0.376 Chirality : 0.037 0.177 2241 Planarity : 0.004 0.036 1475 Dihedral : 30.214 173.963 4161 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.26 % Allowed : 22.28 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.28), residues: 842 helix: 1.25 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.22 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 92 TYR 0.019 0.002 TYR C 50 PHE 0.011 0.002 PHE E 67 TRP 0.007 0.001 TRP K 61 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00536 (13651) covalent geometry : angle 0.65601 (19692) hydrogen bonds : bond 0.05032 ( 791) hydrogen bonds : angle 3.69594 ( 1987) metal coordination : bond 0.00649 ( 8) metal coordination : angle 4.00245 ( 9) link_TRANS : bond 0.00133 ( 2) link_TRANS : angle 0.30273 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7506 (mp0) REVERT: A 93 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8230 (tp40) REVERT: A 125 GLN cc_start: 0.9314 (mp10) cc_final: 0.8862 (mp10) REVERT: B 23 ARG cc_start: 0.8624 (mmp80) cc_final: 0.8096 (mmp80) REVERT: B 63 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: D 34 LYS cc_start: 0.9050 (mptt) cc_final: 0.8762 (mmtm) REVERT: D 57 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8815 (mmmm) REVERT: D 76 GLU cc_start: 0.9320 (tp30) cc_final: 0.9072 (tp30) REVERT: D 79 ARG cc_start: 0.8391 (mtm110) cc_final: 0.7658 (mtm110) REVERT: D 105 GLU cc_start: 0.8586 (tp30) cc_final: 0.7520 (tp30) REVERT: D 120 LYS cc_start: 0.9279 (tttp) cc_final: 0.8888 (ttmm) REVERT: E 60 LEU cc_start: 0.8942 (mm) cc_final: 0.8520 (mm) REVERT: E 68 GLN cc_start: 0.8998 (pp30) cc_final: 0.8687 (pp30) REVERT: E 81 ASP cc_start: 0.8209 (m-30) cc_final: 0.7923 (m-30) REVERT: E 97 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8203 (mt-10) REVERT: E 120 MET cc_start: 0.8172 (mtt) cc_final: 0.7751 (mtp) REVERT: F 43 VAL cc_start: 0.9014 (t) cc_final: 0.8613 (p) REVERT: F 88 TYR cc_start: 0.8660 (m-10) cc_final: 0.7587 (m-10) REVERT: H 68 ASP cc_start: 0.9067 (t70) cc_final: 0.8733 (t0) REVERT: H 83 TYR cc_start: 0.8412 (m-10) cc_final: 0.7337 (m-10) REVERT: H 85 LYS cc_start: 0.9531 (mptt) cc_final: 0.9275 (mmmm) REVERT: H 86 ARG cc_start: 0.9086 (tpp80) cc_final: 0.8873 (tpp80) REVERT: C 24 GLN cc_start: 0.8740 (pm20) cc_final: 0.8313 (pm20) REVERT: C 78 ILE cc_start: 0.9057 (mm) cc_final: 0.8795 (mm) REVERT: C 84 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8641 (tp-100) REVERT: C 91 GLU cc_start: 0.9284 (tp30) cc_final: 0.8937 (tp30) REVERT: C 92 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8122 (mp0) REVERT: G 61 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8657 (mm-30) REVERT: G 90 ASP cc_start: 0.8908 (t0) cc_final: 0.8445 (t0) REVERT: G 104 GLN cc_start: 0.9189 (mp10) cc_final: 0.8713 (mp10) outliers start: 31 outliers final: 19 residues processed: 300 average time/residue: 0.1298 time to fit residues: 53.3113 Evaluate side-chains 293 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 272 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN C 73 ASN C 89 ASN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.076323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.052760 restraints weight = 64707.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.054140 restraints weight = 30327.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055109 restraints weight = 19926.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.055672 restraints weight = 15971.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055873 restraints weight = 14244.715| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13661 Z= 0.168 Angle : 0.643 9.525 19707 Z= 0.364 Chirality : 0.036 0.176 2241 Planarity : 0.004 0.044 1475 Dihedral : 29.965 173.072 4161 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.26 % Allowed : 24.07 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.28), residues: 842 helix: 1.33 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.22 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 92 TYR 0.019 0.002 TYR C 50 PHE 0.008 0.001 PHE H 65 TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00373 (13651) covalent geometry : angle 0.63970 (19692) hydrogen bonds : bond 0.04227 ( 791) hydrogen bonds : angle 3.50684 ( 1987) metal coordination : bond 0.00554 ( 8) metal coordination : angle 3.29736 ( 9) link_TRANS : bond 0.00053 ( 2) link_TRANS : angle 0.24925 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 303 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7390 (mp0) REVERT: A 93 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8316 (tp40) REVERT: A 125 GLN cc_start: 0.9319 (mp10) cc_final: 0.8818 (mp10) REVERT: B 23 ARG cc_start: 0.8660 (mmp80) cc_final: 0.8144 (mmp80) REVERT: B 63 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: B 77 LYS cc_start: 0.9232 (mmtt) cc_final: 0.8300 (mmtt) REVERT: B 84 MET cc_start: 0.8522 (mmm) cc_final: 0.8143 (tpp) REVERT: D 34 LYS cc_start: 0.9049 (mptt) cc_final: 0.8752 (mmtm) REVERT: D 57 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8759 (mmmm) REVERT: D 59 MET cc_start: 0.9264 (tpp) cc_final: 0.9002 (tpp) REVERT: D 76 GLU cc_start: 0.9326 (tp30) cc_final: 0.9095 (tp30) REVERT: D 92 ARG cc_start: 0.8822 (ttp80) cc_final: 0.8175 (ttp80) REVERT: D 105 GLU cc_start: 0.8557 (tp30) cc_final: 0.7480 (tp30) REVERT: D 120 LYS cc_start: 0.9285 (tttp) cc_final: 0.8935 (ttmm) REVERT: E 60 LEU cc_start: 0.8859 (mm) cc_final: 0.8311 (mm) REVERT: E 68 GLN cc_start: 0.8868 (pp30) cc_final: 0.8554 (pp30) REVERT: E 81 ASP cc_start: 0.8076 (m-30) cc_final: 0.7792 (m-30) REVERT: E 93 GLN cc_start: 0.9575 (tt0) cc_final: 0.9238 (tt0) REVERT: E 120 MET cc_start: 0.8074 (mtt) cc_final: 0.7751 (mtp) REVERT: F 43 VAL cc_start: 0.8991 (t) cc_final: 0.8628 (p) REVERT: F 88 TYR cc_start: 0.8573 (m-10) cc_final: 0.7508 (m-10) REVERT: H 68 ASP cc_start: 0.9033 (t70) cc_final: 0.8740 (t0) REVERT: H 83 TYR cc_start: 0.8420 (m-10) cc_final: 0.7435 (m-10) REVERT: H 86 ARG cc_start: 0.9033 (tpp80) cc_final: 0.8811 (tpp80) REVERT: K 35 LEU cc_start: 0.7187 (pt) cc_final: 0.6963 (pt) REVERT: C 24 GLN cc_start: 0.8852 (pm20) cc_final: 0.8470 (pm20) REVERT: C 78 ILE cc_start: 0.9003 (mm) cc_final: 0.8782 (mm) REVERT: C 84 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8385 (tp-100) REVERT: C 91 GLU cc_start: 0.9296 (tp30) cc_final: 0.8801 (tp30) REVERT: C 92 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8111 (mp0) REVERT: G 90 ASP cc_start: 0.8879 (t0) cc_final: 0.8650 (t0) REVERT: G 104 GLN cc_start: 0.9197 (mp10) cc_final: 0.8755 (mp10) outliers start: 31 outliers final: 14 residues processed: 312 average time/residue: 0.1349 time to fit residues: 57.9664 Evaluate side-chains 293 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 277 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN C 73 ASN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.074772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.050365 restraints weight = 79087.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052015 restraints weight = 33709.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.052988 restraints weight = 21482.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.053599 restraints weight = 16950.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053799 restraints weight = 14991.602| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13661 Z= 0.235 Angle : 0.664 8.232 19707 Z= 0.378 Chirality : 0.038 0.181 2241 Planarity : 0.005 0.051 1475 Dihedral : 30.082 172.560 4161 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.26 % Allowed : 26.41 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.28), residues: 842 helix: 1.33 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 92 TYR 0.025 0.002 TYR H 40 PHE 0.020 0.002 PHE E 67 TRP 0.008 0.001 TRP K 61 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00533 (13651) covalent geometry : angle 0.66048 (19692) hydrogen bonds : bond 0.04972 ( 791) hydrogen bonds : angle 3.69420 ( 1987) metal coordination : bond 0.00724 ( 8) metal coordination : angle 3.30741 ( 9) link_TRANS : bond 0.00142 ( 2) link_TRANS : angle 0.29888 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8279 (tp40) REVERT: A 125 GLN cc_start: 0.9285 (mp10) cc_final: 0.8789 (mp10) REVERT: B 23 ARG cc_start: 0.8634 (mmp80) cc_final: 0.8391 (mmp80) REVERT: B 25 ASN cc_start: 0.8837 (m110) cc_final: 0.8343 (m-40) REVERT: B 59 LYS cc_start: 0.9439 (ttmm) cc_final: 0.8826 (ttmm) REVERT: B 84 MET cc_start: 0.8627 (mmm) cc_final: 0.8071 (tpp) REVERT: D 34 LYS cc_start: 0.9081 (mptt) cc_final: 0.8768 (mmtm) REVERT: D 57 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8819 (mmmm) REVERT: D 59 MET cc_start: 0.9275 (tpp) cc_final: 0.8973 (tpp) REVERT: D 76 GLU cc_start: 0.9258 (tp30) cc_final: 0.8577 (tp30) REVERT: D 79 ARG cc_start: 0.8705 (ttp-110) cc_final: 0.8177 (ttp-110) REVERT: D 105 GLU cc_start: 0.8595 (tp30) cc_final: 0.7641 (tp30) REVERT: D 120 LYS cc_start: 0.9279 (tttp) cc_final: 0.8931 (ttmm) REVERT: E 60 LEU cc_start: 0.8861 (mm) cc_final: 0.8199 (mm) REVERT: E 68 GLN cc_start: 0.8994 (pp30) cc_final: 0.8661 (pp30) REVERT: E 81 ASP cc_start: 0.8141 (m-30) cc_final: 0.7858 (m-30) REVERT: E 97 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8085 (mt-10) REVERT: E 120 MET cc_start: 0.8234 (mtt) cc_final: 0.7880 (mtp) REVERT: E 133 GLU cc_start: 0.7347 (pm20) cc_final: 0.6947 (pm20) REVERT: F 43 VAL cc_start: 0.9098 (t) cc_final: 0.8776 (p) REVERT: F 88 TYR cc_start: 0.8632 (m-10) cc_final: 0.7606 (m-10) REVERT: H 68 ASP cc_start: 0.9077 (t70) cc_final: 0.8717 (t0) REVERT: H 83 TYR cc_start: 0.8418 (m-10) cc_final: 0.7388 (m-10) REVERT: H 86 ARG cc_start: 0.9086 (tpp80) cc_final: 0.8884 (tpp80) REVERT: C 56 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8336 (mt-10) REVERT: C 78 ILE cc_start: 0.9046 (mm) cc_final: 0.8800 (mm) REVERT: C 84 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8297 (tp-100) REVERT: C 91 GLU cc_start: 0.9318 (tp30) cc_final: 0.8941 (tp30) REVERT: C 92 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8127 (mp0) REVERT: G 90 ASP cc_start: 0.8882 (t0) cc_final: 0.8679 (t0) REVERT: G 104 GLN cc_start: 0.9211 (mp10) cc_final: 0.8722 (mp10) outliers start: 31 outliers final: 16 residues processed: 295 average time/residue: 0.1304 time to fit residues: 52.8332 Evaluate side-chains 287 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 270 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS C 38 ASN C 73 ASN G 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.075971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051629 restraints weight = 108931.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.053407 restraints weight = 38816.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.054585 restraints weight = 22730.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.055297 restraints weight = 17080.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.055669 restraints weight = 14700.248| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13661 Z= 0.180 Angle : 0.670 10.104 19707 Z= 0.378 Chirality : 0.037 0.175 2241 Planarity : 0.004 0.046 1475 Dihedral : 29.973 172.122 4161 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.26 % Allowed : 28.75 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.28), residues: 842 helix: 1.29 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -1.36 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 92 TYR 0.026 0.002 TYR H 40 PHE 0.016 0.002 PHE H 65 TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00402 (13651) covalent geometry : angle 0.66505 (19692) hydrogen bonds : bond 0.04395 ( 791) hydrogen bonds : angle 3.64030 ( 1987) metal coordination : bond 0.00606 ( 8) metal coordination : angle 3.89539 ( 9) link_TRANS : bond 0.00064 ( 2) link_TRANS : angle 0.22834 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8287 (tp40) REVERT: A 105 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: A 125 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.8797 (mp10) REVERT: B 23 ARG cc_start: 0.8583 (mmp80) cc_final: 0.8124 (mmp80) REVERT: B 77 LYS cc_start: 0.9181 (mmtt) cc_final: 0.8807 (mmtt) REVERT: B 84 MET cc_start: 0.8631 (mmm) cc_final: 0.8201 (tpp) REVERT: B 88 TYR cc_start: 0.8678 (m-80) cc_final: 0.8335 (m-80) REVERT: D 34 LYS cc_start: 0.9090 (mptt) cc_final: 0.8757 (mmtm) REVERT: D 47 GLN cc_start: 0.8809 (mt0) cc_final: 0.8462 (mt0) REVERT: D 57 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8772 (mmmm) REVERT: D 59 MET cc_start: 0.9265 (tpp) cc_final: 0.8985 (tpp) REVERT: D 92 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8030 (ttp80) REVERT: D 105 GLU cc_start: 0.8574 (tp30) cc_final: 0.7578 (tp30) REVERT: D 120 LYS cc_start: 0.9253 (tttp) cc_final: 0.8904 (ttmm) REVERT: E 60 LEU cc_start: 0.8839 (mm) cc_final: 0.8205 (mm) REVERT: E 68 GLN cc_start: 0.8958 (pp30) cc_final: 0.8660 (pp30) REVERT: E 81 ASP cc_start: 0.8067 (m-30) cc_final: 0.7796 (m-30) REVERT: E 97 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7936 (mt-10) REVERT: E 120 MET cc_start: 0.8175 (mtt) cc_final: 0.7804 (mtp) REVERT: F 43 VAL cc_start: 0.9066 (t) cc_final: 0.8766 (p) REVERT: F 88 TYR cc_start: 0.8568 (m-10) cc_final: 0.7544 (m-10) REVERT: H 68 ASP cc_start: 0.9063 (t70) cc_final: 0.8721 (t0) REVERT: H 83 TYR cc_start: 0.8369 (m-10) cc_final: 0.7208 (m-10) REVERT: H 86 ARG cc_start: 0.9046 (tpp80) cc_final: 0.8814 (tpp80) REVERT: H 93 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8566 (mm-30) REVERT: C 78 ILE cc_start: 0.9009 (mm) cc_final: 0.8745 (mm) REVERT: C 84 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8202 (tp-100) REVERT: C 91 GLU cc_start: 0.9334 (tp30) cc_final: 0.8966 (tp30) REVERT: C 92 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8057 (mp0) REVERT: G 90 ASP cc_start: 0.8905 (t0) cc_final: 0.8611 (t0) REVERT: G 104 GLN cc_start: 0.9202 (mp10) cc_final: 0.8748 (mp10) outliers start: 31 outliers final: 14 residues processed: 304 average time/residue: 0.1389 time to fit residues: 57.9338 Evaluate side-chains 293 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 48 optimal weight: 0.0070 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 40 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.076529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.052263 restraints weight = 97683.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.053852 restraints weight = 36770.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.054972 restraints weight = 21861.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055638 restraints weight = 16688.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055869 restraints weight = 14467.327| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13661 Z= 0.179 Angle : 0.686 11.432 19707 Z= 0.383 Chirality : 0.038 0.304 2241 Planarity : 0.004 0.046 1475 Dihedral : 29.912 171.582 4161 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.44 % Allowed : 30.12 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.28), residues: 842 helix: 1.26 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -1.38 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 92 TYR 0.025 0.002 TYR H 40 PHE 0.016 0.001 PHE H 65 TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00400 (13651) covalent geometry : angle 0.68187 (19692) hydrogen bonds : bond 0.04413 ( 791) hydrogen bonds : angle 3.63822 ( 1987) metal coordination : bond 0.00624 ( 8) metal coordination : angle 3.64835 ( 9) link_TRANS : bond 0.00086 ( 2) link_TRANS : angle 0.23669 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 292 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8937 (mmp) cc_final: 0.8665 (mmp) REVERT: A 93 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8323 (tp40) REVERT: A 105 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8381 (mm-30) REVERT: A 125 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8828 (mp10) REVERT: B 23 ARG cc_start: 0.8533 (mmp80) cc_final: 0.8107 (mmp80) REVERT: B 77 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8478 (mmtt) REVERT: B 84 MET cc_start: 0.8644 (mmm) cc_final: 0.8248 (tpp) REVERT: B 88 TYR cc_start: 0.8653 (m-80) cc_final: 0.8286 (m-80) REVERT: D 34 LYS cc_start: 0.9083 (mptt) cc_final: 0.8753 (mmtm) REVERT: D 57 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8767 (mmmm) REVERT: D 59 MET cc_start: 0.9248 (tpp) cc_final: 0.8964 (tpp) REVERT: D 76 GLU cc_start: 0.9138 (tp30) cc_final: 0.8390 (tp30) REVERT: D 79 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8113 (ttp-110) REVERT: D 92 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8086 (ttp80) REVERT: D 96 THR cc_start: 0.9539 (m) cc_final: 0.9339 (p) REVERT: D 105 GLU cc_start: 0.8531 (tp30) cc_final: 0.7585 (tp30) REVERT: D 120 LYS cc_start: 0.9215 (tttp) cc_final: 0.8873 (ttmm) REVERT: E 52 ARG cc_start: 0.8817 (mtm-85) cc_final: 0.8151 (mtm-85) REVERT: E 60 LEU cc_start: 0.8772 (mm) cc_final: 0.8423 (mp) REVERT: E 67 PHE cc_start: 0.9240 (t80) cc_final: 0.8951 (t80) REVERT: E 68 GLN cc_start: 0.8925 (pp30) cc_final: 0.8605 (pp30) REVERT: E 81 ASP cc_start: 0.8045 (m-30) cc_final: 0.7762 (m-30) REVERT: E 120 MET cc_start: 0.8161 (mtt) cc_final: 0.7773 (mtp) REVERT: F 43 VAL cc_start: 0.8927 (t) cc_final: 0.8611 (p) REVERT: F 88 TYR cc_start: 0.8639 (m-10) cc_final: 0.7560 (m-10) REVERT: H 68 ASP cc_start: 0.9039 (t70) cc_final: 0.8696 (t0) REVERT: H 83 TYR cc_start: 0.8439 (m-10) cc_final: 0.7189 (m-10) REVERT: H 86 ARG cc_start: 0.9009 (tpp80) cc_final: 0.8783 (tpp80) REVERT: H 93 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8601 (mm-30) REVERT: C 78 ILE cc_start: 0.9009 (mm) cc_final: 0.8772 (mm) REVERT: C 84 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8198 (tp-100) REVERT: C 91 GLU cc_start: 0.9322 (tp30) cc_final: 0.8852 (tp30) REVERT: C 92 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8191 (mp0) REVERT: G 104 GLN cc_start: 0.9181 (mp10) cc_final: 0.8738 (mp10) outliers start: 25 outliers final: 15 residues processed: 298 average time/residue: 0.1422 time to fit residues: 57.8911 Evaluate side-chains 299 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 281 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.076189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.052056 restraints weight = 91103.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.053821 restraints weight = 35514.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.054878 restraints weight = 21626.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.055532 restraints weight = 16731.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.055769 restraints weight = 14557.409| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13661 Z= 0.187 Angle : 0.692 12.854 19707 Z= 0.387 Chirality : 0.038 0.190 2241 Planarity : 0.004 0.049 1475 Dihedral : 29.903 171.437 4161 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.44 % Allowed : 29.71 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.28), residues: 842 helix: 1.29 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -1.33 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 92 TYR 0.025 0.002 TYR G 57 PHE 0.028 0.002 PHE H 65 TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00419 (13651) covalent geometry : angle 0.68798 (19692) hydrogen bonds : bond 0.04480 ( 791) hydrogen bonds : angle 3.63404 ( 1987) metal coordination : bond 0.00644 ( 8) metal coordination : angle 3.55866 ( 9) link_TRANS : bond 0.00099 ( 2) link_TRANS : angle 0.27356 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8329 (tp40) REVERT: A 105 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8367 (mm-30) REVERT: A 125 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8811 (mp10) REVERT: B 77 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8624 (mmtt) REVERT: B 84 MET cc_start: 0.8670 (mmm) cc_final: 0.8289 (tpp) REVERT: B 88 TYR cc_start: 0.8696 (m-80) cc_final: 0.8366 (m-80) REVERT: D 34 LYS cc_start: 0.9033 (mptt) cc_final: 0.8732 (mmtm) REVERT: D 57 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8772 (mmmm) REVERT: D 59 MET cc_start: 0.9250 (tpp) cc_final: 0.8933 (tpp) REVERT: D 92 ARG cc_start: 0.8812 (ttp80) cc_final: 0.7993 (ttp80) REVERT: D 96 THR cc_start: 0.9526 (m) cc_final: 0.9313 (p) REVERT: D 105 GLU cc_start: 0.8539 (tp30) cc_final: 0.7593 (tp30) REVERT: D 120 LYS cc_start: 0.9227 (tttp) cc_final: 0.8878 (ttmm) REVERT: E 52 ARG cc_start: 0.8793 (mtm-85) cc_final: 0.8137 (mtm-85) REVERT: E 60 LEU cc_start: 0.8722 (mm) cc_final: 0.8377 (mp) REVERT: E 68 GLN cc_start: 0.8969 (pp30) cc_final: 0.8625 (pp30) REVERT: E 81 ASP cc_start: 0.8039 (m-30) cc_final: 0.7749 (m-30) REVERT: E 120 MET cc_start: 0.8089 (mtt) cc_final: 0.7788 (mtp) REVERT: F 43 VAL cc_start: 0.8950 (t) cc_final: 0.8662 (p) REVERT: F 88 TYR cc_start: 0.8672 (m-10) cc_final: 0.7695 (m-10) REVERT: H 68 ASP cc_start: 0.9047 (t70) cc_final: 0.8677 (t0) REVERT: H 83 TYR cc_start: 0.8440 (m-10) cc_final: 0.7329 (m-10) REVERT: H 86 ARG cc_start: 0.9012 (tpp80) cc_final: 0.8792 (tpp80) REVERT: H 93 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8642 (mm-30) REVERT: C 78 ILE cc_start: 0.9017 (mm) cc_final: 0.8764 (mm) REVERT: C 84 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8142 (tp-100) REVERT: C 91 GLU cc_start: 0.9343 (tp30) cc_final: 0.8967 (tp30) REVERT: C 92 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8126 (mp0) REVERT: G 104 GLN cc_start: 0.9188 (mp10) cc_final: 0.8724 (mp10) outliers start: 25 outliers final: 18 residues processed: 290 average time/residue: 0.1420 time to fit residues: 56.3129 Evaluate side-chains 300 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 279 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 87 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.0170 chunk 92 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 89 ASN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.075453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.050917 restraints weight = 73944.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052522 restraints weight = 33016.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.053498 restraints weight = 21505.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.053800 restraints weight = 17127.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.054310 restraints weight = 15727.940| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13661 Z= 0.228 Angle : 0.718 12.540 19707 Z= 0.400 Chirality : 0.040 0.267 2241 Planarity : 0.005 0.049 1475 Dihedral : 30.004 171.818 4161 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.03 % Allowed : 30.54 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.29), residues: 842 helix: 1.23 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 92 TYR 0.029 0.002 TYR G 57 PHE 0.026 0.002 PHE H 65 TRP 0.008 0.001 TRP K 61 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00515 (13651) covalent geometry : angle 0.71406 (19692) hydrogen bonds : bond 0.04975 ( 791) hydrogen bonds : angle 3.75684 ( 1987) metal coordination : bond 0.00671 ( 8) metal coordination : angle 3.75156 ( 9) link_TRANS : bond 0.00149 ( 2) link_TRANS : angle 0.34760 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 277 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8364 (tp40) REVERT: A 105 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: A 125 GLN cc_start: 0.9313 (mp10) cc_final: 0.8804 (mp10) REVERT: B 84 MET cc_start: 0.8699 (mmm) cc_final: 0.8155 (tpp) REVERT: B 88 TYR cc_start: 0.8808 (m-80) cc_final: 0.8606 (m-80) REVERT: D 34 LYS cc_start: 0.9023 (mptt) cc_final: 0.8720 (mmtm) REVERT: D 57 LYS cc_start: 0.9110 (mmtt) cc_final: 0.8816 (mmmm) REVERT: D 105 GLU cc_start: 0.8550 (tp30) cc_final: 0.7649 (tp30) REVERT: D 120 LYS cc_start: 0.9238 (tttp) cc_final: 0.8896 (ttmm) REVERT: E 52 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8142 (mtm-85) REVERT: E 60 LEU cc_start: 0.8738 (mm) cc_final: 0.8488 (mp) REVERT: E 68 GLN cc_start: 0.8986 (pp30) cc_final: 0.8611 (pp30) REVERT: E 81 ASP cc_start: 0.8054 (m-30) cc_final: 0.7776 (m-30) REVERT: E 120 MET cc_start: 0.8060 (mtt) cc_final: 0.7602 (mtp) REVERT: E 133 GLU cc_start: 0.7358 (pm20) cc_final: 0.7005 (pm20) REVERT: F 43 VAL cc_start: 0.9001 (t) cc_final: 0.8725 (p) REVERT: F 88 TYR cc_start: 0.8682 (m-10) cc_final: 0.7736 (m-10) REVERT: H 68 ASP cc_start: 0.9078 (t70) cc_final: 0.8693 (t0) REVERT: H 83 TYR cc_start: 0.8471 (m-10) cc_final: 0.7491 (m-10) REVERT: H 86 ARG cc_start: 0.9033 (tpp80) cc_final: 0.8831 (tpp80) REVERT: C 78 ILE cc_start: 0.9057 (mm) cc_final: 0.8758 (mm) REVERT: C 84 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8147 (tp-100) REVERT: C 91 GLU cc_start: 0.9329 (tp30) cc_final: 0.8892 (tp30) REVERT: C 92 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8164 (mp0) REVERT: G 104 GLN cc_start: 0.9238 (mp10) cc_final: 0.8754 (mp10) outliers start: 22 outliers final: 15 residues processed: 283 average time/residue: 0.1434 time to fit residues: 55.3825 Evaluate side-chains 293 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 87 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 89 ASN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.076347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.051602 restraints weight = 86431.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053301 restraints weight = 35212.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.054385 restraints weight = 21900.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.055005 restraints weight = 17046.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.055326 restraints weight = 14984.839| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13661 Z= 0.188 Angle : 0.712 10.425 19707 Z= 0.396 Chirality : 0.039 0.231 2241 Planarity : 0.005 0.048 1475 Dihedral : 29.952 171.581 4161 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.48 % Allowed : 31.77 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.28), residues: 842 helix: 1.12 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.29 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 79 TYR 0.033 0.002 TYR F 98 PHE 0.027 0.002 PHE H 65 TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00423 (13651) covalent geometry : angle 0.70747 (19692) hydrogen bonds : bond 0.04503 ( 791) hydrogen bonds : angle 3.69533 ( 1987) metal coordination : bond 0.00644 ( 8) metal coordination : angle 3.64895 ( 9) link_TRANS : bond 0.00100 ( 2) link_TRANS : angle 0.33445 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.63 seconds wall clock time: 48 minutes 35.32 seconds (2915.32 seconds total)