Starting phenix.real_space_refine on Thu Feb 5 09:25:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9od3_70339/02_2026/9od3_70339_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9od3_70339/02_2026/9od3_70339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9od3_70339/02_2026/9od3_70339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9od3_70339/02_2026/9od3_70339.map" model { file = "/net/cci-nas-00/data/ceres_data/9od3_70339/02_2026/9od3_70339_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9od3_70339/02_2026/9od3_70339_trim.cif" } resolution = 2.94 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 ------------------------------------------------------------------------------- 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= -0.011 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 5289 2.51 5 N 1406 2.21 5 O 1613 1.98 5 H 8062 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16415 Number of models: 1 Model: "" Number of chains: 7 Chain: "1" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4349 Classifications: {'peptide': 278} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 255} Chain: "2" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4049 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 245} Chain: "3" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3604 Classifications: {'peptide': 235} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 216} Chain: "4" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 892 Classifications: {'peptide': 59} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "H" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1939 Classifications: {'peptide': 129} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1564 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "1" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.96, per 1000 atoms: 0.18 Number of scatterers: 16415 At special positions: 0 Unit cell: (103.4, 118.8, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 O 1613 8.00 N 1406 7.00 C 5289 6.00 H 8062 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 539.9 milliseconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 18 sheets defined 13.1% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain '1' and resid 46 through 50 Processing helix chain '1' and resid 56 through 60 Processing helix chain '1' and resid 72 through 75 Processing helix chain '1' and resid 76 through 82 Processing helix chain '1' and resid 116 through 123 Processing helix chain '1' and resid 172 through 177 removed outlier: 3.531A pdb=" N TRP 1 175 " --> pdb=" O ASP 1 172 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR 1 177 " --> pdb=" O THR 1 174 " (cutoff:3.500A) Processing helix chain '1' and resid 222 through 226 removed outlier: 3.515A pdb=" N ILE 1 225 " --> pdb=" O ASN 1 222 " (cutoff:3.500A) Processing helix chain '2' and resid 35 through 37 No H-bonds generated for 'chain '2' and resid 35 through 37' Processing helix chain '2' and resid 43 through 47 Processing helix chain '2' and resid 56 through 60 removed outlier: 3.551A pdb=" N ALA 2 59 " --> pdb=" O PRO 2 56 " (cutoff:3.500A) Processing helix chain '2' and resid 83 through 87 Processing helix chain '2' and resid 89 through 99 removed outlier: 3.681A pdb=" N GLY 2 93 " --> pdb=" O MET 2 89 " (cutoff:3.500A) Processing helix chain '2' and resid 143 through 148 Processing helix chain '2' and resid 176 through 180 Processing helix chain '2' and resid 185 through 192 removed outlier: 4.321A pdb=" N PHE 2 190 " --> pdb=" O GLY 2 187 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 48 Processing helix chain '3' and resid 64 through 69 removed outlier: 3.613A pdb=" N TYR 3 68 " --> pdb=" O MET 3 65 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG 3 69 " --> pdb=" O ASP 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 98 through 105 Processing helix chain '3' and resid 144 through 149 Processing helix chain '4' and resid 35 through 39 Processing helix chain '4' and resid 50 through 55 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.689A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain '1' and resid 44 through 45 removed outlier: 3.550A pdb=" N THR 3 51 " --> pdb=" O VAL 3 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain '1' and resid 85 through 94 removed outlier: 5.844A pdb=" N CYS 1 86 " --> pdb=" O MET 1 262 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET 1 262 " --> pdb=" O CYS 1 86 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA 1 88 " --> pdb=" O ILE 1 260 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL 1 267 " --> pdb=" O ARG 1 129 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG 1 129 " --> pdb=" O VAL 1 267 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL 1 269 " --> pdb=" O TYR 1 127 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR 1 127 " --> pdb=" O VAL 1 269 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N CYS 1 271 " --> pdb=" O PHE 1 125 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE 1 125 " --> pdb=" O CYS 1 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 192 through 196 removed outlier: 3.611A pdb=" N ALA 1 192 " --> pdb=" O PHE 1 136 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE 1 125 " --> pdb=" O CYS 1 271 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N CYS 1 271 " --> pdb=" O PHE 1 125 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR 1 127 " --> pdb=" O VAL 1 269 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL 1 269 " --> pdb=" O TYR 1 127 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG 1 129 " --> pdb=" O VAL 1 267 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL 1 267 " --> pdb=" O ARG 1 129 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL 1 269 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 105 through 109 Processing sheet with id=AA6, first strand: chain '2' and resid 14 through 18 Processing sheet with id=AA7, first strand: chain '2' and resid 31 through 33 removed outlier: 6.859A pdb=" N VAL 2 32 " --> pdb=" O VAL 2 208 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG 2 103 " --> pdb=" O SER 2 257 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER 2 257 " --> pdb=" O ARG 2 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 31 through 33 removed outlier: 6.859A pdb=" N VAL 2 32 " --> pdb=" O VAL 2 208 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG 2 103 " --> pdb=" O SER 2 257 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER 2 257 " --> pdb=" O ARG 2 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 154 through 155 removed outlier: 3.520A pdb=" N TRP 2 79 " --> pdb=" O GLY 2 154 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP 2 226 " --> pdb=" O LEU 2 82 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA 2 121 " --> pdb=" O LEU 2 233 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN 2 119 " --> pdb=" O PRO 2 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 83 through 86 removed outlier: 4.169A pdb=" N LEU 3 83 " --> pdb=" O MET 3 192 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS 3 129 " --> pdb=" O GLN 3 195 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG 3 197 " --> pdb=" O THR 3 127 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR 3 127 " --> pdb=" O ARG 3 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 177 through 178 Processing sheet with id=AB3, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.509A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.878A pdb=" N VAL H 118 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.564A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP L 41 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.564A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR L 115 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 19 through 24 287 hydrogen bonds defined for protein. 681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8049 1.03 - 1.23: 20 1.23 - 1.42: 3678 1.42 - 1.62: 4809 1.62 - 1.81: 73 Bond restraints: 16629 Sorted by residual: bond pdb=" N ASP 1 25 " pdb=" CA ASP 1 25 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N TYR 2 9 " pdb=" CA TYR 2 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N ASP 1 25 " pdb=" H ASP 1 25 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" N TYR 2 9 " pdb=" H TYR 2 9 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CA VAL 1 278 " pdb=" CB VAL 1 278 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 9.30e-01 ... (remaining 16624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 27768 1.00 - 2.01: 2001 2.01 - 3.01: 89 3.01 - 4.01: 49 4.01 - 5.02: 5 Bond angle restraints: 29912 Sorted by residual: angle pdb=" N LYS 2 170 " pdb=" CA LYS 2 170 " pdb=" CB LYS 2 170 " ideal model delta sigma weight residual 114.17 109.15 5.02 1.14e+00 7.69e-01 1.94e+01 angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.20 110.34 2.86 9.60e-01 1.09e+00 8.88e+00 angle pdb=" N GLY 2 77 " pdb=" CA GLY 2 77 " pdb=" C GLY 2 77 " ideal model delta sigma weight residual 110.56 113.91 -3.35 1.36e+00 5.41e-01 6.08e+00 angle pdb=" C VAL 1 285 " pdb=" CA VAL 1 285 " pdb=" CB VAL 1 285 " ideal model delta sigma weight residual 112.19 109.44 2.75 1.15e+00 7.56e-01 5.72e+00 angle pdb=" N ARG 3 223 " pdb=" CA ARG 3 223 " pdb=" C ARG 3 223 " ideal model delta sigma weight residual 112.12 115.30 -3.18 1.34e+00 5.57e-01 5.62e+00 ... (remaining 29907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 7429 17.03 - 34.06: 374 34.06 - 51.10: 136 51.10 - 68.13: 56 68.13 - 85.16: 12 Dihedral angle restraints: 8007 sinusoidal: 4278 harmonic: 3729 Sorted by residual: dihedral pdb=" CA ARG 1 288 " pdb=" C ARG 1 288 " pdb=" N ASN 1 289 " pdb=" CA ASN 1 289 " ideal model delta harmonic sigma weight residual -180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASN 1 289 " pdb=" C ASN 1 289 " pdb=" N ASN 1 290 " pdb=" CA ASN 1 290 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 62.66 30.34 1 1.00e+01 1.00e-02 1.31e+01 ... (remaining 8004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 687 0.028 - 0.055: 405 0.055 - 0.083: 80 0.083 - 0.110: 57 0.110 - 0.138: 54 Chirality restraints: 1283 Sorted by residual: chirality pdb=" CA ARG 3 223 " pdb=" N ARG 3 223 " pdb=" C ARG 3 223 " pdb=" CB ARG 3 223 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE 3 53 " pdb=" N ILE 3 53 " pdb=" C ILE 3 53 " pdb=" CB ILE 3 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE 1 194 " pdb=" N ILE 1 194 " pdb=" C ILE 1 194 " pdb=" CB ILE 1 194 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1280 not shown) Planarity restraints: 2507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP 2 38 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO 2 39 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO 2 39 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 2 39 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA 1 190 " 0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO 1 191 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO 1 191 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO 1 191 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 1 196 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO 1 197 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO 1 197 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO 1 197 " -0.020 5.00e-02 4.00e+02 ... (remaining 2504 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 434 2.16 - 2.77: 30349 2.77 - 3.38: 41114 3.38 - 3.99: 55429 3.99 - 4.60: 86878 Nonbonded interactions: 214204 Sorted by model distance: nonbonded pdb=" O ASP L 29 " pdb=" H GLY L 35 " model vdw 1.548 2.450 nonbonded pdb="HH12 ARG 1 288 " pdb=" OD1 ASP 2 137 " model vdw 1.584 2.450 nonbonded pdb=" OD1 ASN 1 146 " pdb="HD21 ASN 1 147 " model vdw 1.613 2.450 nonbonded pdb=" O GLN 3 195 " pdb=" HG1 THR 3 196 " model vdw 1.658 2.450 nonbonded pdb=" O PRO L 7 " pdb=" HG1 THR L 122 " model vdw 1.670 2.450 ... (remaining 214199 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 32.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.560 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 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 : 0.003 0.032 8569 Z= 0.150 Angle : 0.546 5.017 11671 Z= 0.316 Chirality : 0.044 0.138 1283 Planarity : 0.004 0.036 1508 Dihedral : 10.967 85.162 3087 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.25), residues: 1058 helix: -1.42 (0.67), residues: 63 sheet: 0.82 (0.28), residues: 319 loop : -0.81 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 87 TYR 0.011 0.001 TYR H 103 PHE 0.011 0.001 PHE 2 173 TRP 0.013 0.001 TRP 1 270 HIS 0.006 0.001 HIS 1 249 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8567) covalent geometry : angle 0.54582 (11667) SS BOND : bond 0.00275 ( 2) SS BOND : angle 0.43350 ( 4) hydrogen bonds : bond 0.23664 ( 240) hydrogen bonds : angle 8.00670 ( 681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 112 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 69 ARG cc_start: 0.8775 (mtt180) cc_final: 0.7784 (ptm160) REVERT: 3 147 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8731 (mt-10) REVERT: 3 149 MET cc_start: 0.8777 (ptm) cc_final: 0.8446 (ptm) REVERT: H 31 ASP cc_start: 0.7150 (t70) cc_final: 0.6642 (t0) REVERT: L 95 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6945 (mt0) REVERT: L 99 GLU cc_start: 0.8622 (tt0) cc_final: 0.7856 (tp30) REVERT: L 124 VAL cc_start: 0.8888 (t) cc_final: 0.8012 (t) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 1.5718 time to fit residues: 201.6795 Evaluate side-chains 79 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.075050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.058132 restraints weight = 54430.545| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.26 r_work: 0.2699 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8569 Z= 0.101 Angle : 0.510 4.329 11671 Z= 0.273 Chirality : 0.044 0.177 1283 Planarity : 0.004 0.035 1508 Dihedral : 4.589 28.924 1185 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.79 % Rotamer: Outliers : 0.54 % Allowed : 4.35 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1058 helix: -1.48 (0.65), residues: 63 sheet: 1.22 (0.29), residues: 314 loop : -0.78 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 3 69 TYR 0.009 0.001 TYR 3 194 PHE 0.010 0.001 PHE 2 173 TRP 0.010 0.001 TRP 1 270 HIS 0.002 0.001 HIS 3 153 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8567) covalent geometry : angle 0.51025 (11667) SS BOND : bond 0.00525 ( 2) SS BOND : angle 0.77120 ( 4) hydrogen bonds : bond 0.04699 ( 240) hydrogen bonds : angle 5.34674 ( 681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 112 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 69 ARG cc_start: 0.8739 (mtt180) cc_final: 0.7741 (ptm160) REVERT: 3 147 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8748 (mt-10) REVERT: 3 149 MET cc_start: 0.8774 (ptm) cc_final: 0.8446 (ptm) REVERT: H 31 ASP cc_start: 0.6970 (t70) cc_final: 0.6367 (t0) REVERT: H 89 GLU cc_start: 0.8202 (mp0) cc_final: 0.7975 (pm20) REVERT: L 99 GLU cc_start: 0.8665 (tt0) cc_final: 0.7986 (tt0) REVERT: L 123 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8286 (tttp) REVERT: L 124 VAL cc_start: 0.8930 (t) cc_final: 0.8411 (p) outliers start: 5 outliers final: 1 residues processed: 84 average time/residue: 1.4132 time to fit residues: 125.8236 Evaluate side-chains 77 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.057587 restraints weight = 54783.937| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.22 r_work: 0.2689 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8569 Z= 0.117 Angle : 0.494 4.126 11671 Z= 0.262 Chirality : 0.044 0.160 1283 Planarity : 0.004 0.050 1508 Dihedral : 4.551 27.926 1185 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.33 % Allowed : 5.55 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1058 helix: -1.76 (0.61), residues: 70 sheet: 1.22 (0.28), residues: 314 loop : -0.91 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 100 TYR 0.008 0.001 TYR 1 205 PHE 0.009 0.001 PHE 2 173 TRP 0.007 0.001 TRP 1 270 HIS 0.003 0.001 HIS 1 249 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8567) covalent geometry : angle 0.49364 (11667) SS BOND : bond 0.00445 ( 2) SS BOND : angle 0.68641 ( 4) hydrogen bonds : bond 0.03973 ( 240) hydrogen bonds : angle 4.92424 ( 681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 112 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 69 ARG cc_start: 0.8738 (mtt180) cc_final: 0.7765 (ptm160) REVERT: 3 147 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8733 (mt-10) REVERT: 3 149 MET cc_start: 0.8830 (ptm) cc_final: 0.8462 (ptm) REVERT: H 31 ASP cc_start: 0.7010 (t70) cc_final: 0.6280 (t0) REVERT: L 99 GLU cc_start: 0.8671 (tt0) cc_final: 0.8105 (tt0) REVERT: L 123 LYS cc_start: 0.8790 (ttpp) cc_final: 0.8341 (tttp) outliers start: 3 outliers final: 0 residues processed: 79 average time/residue: 1.4622 time to fit residues: 122.4112 Evaluate side-chains 74 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 0.0010 chunk 53 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.058921 restraints weight = 53973.517| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.28 r_work: 0.2711 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8569 Z= 0.082 Angle : 0.468 4.489 11671 Z= 0.245 Chirality : 0.043 0.159 1283 Planarity : 0.004 0.042 1508 Dihedral : 4.341 27.712 1185 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.33 % Allowed : 6.20 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1058 helix: -1.72 (0.62), residues: 70 sheet: 1.19 (0.28), residues: 316 loop : -0.78 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 100 TYR 0.006 0.001 TYR 1 205 PHE 0.007 0.001 PHE 2 173 TRP 0.006 0.001 TRP 1 270 HIS 0.003 0.000 HIS 1 249 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 8567) covalent geometry : angle 0.46816 (11667) SS BOND : bond 0.00393 ( 2) SS BOND : angle 0.58601 ( 4) hydrogen bonds : bond 0.03180 ( 240) hydrogen bonds : angle 4.63820 ( 681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 112 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 39 LYS cc_start: 0.6460 (OUTLIER) cc_final: 0.5137 (mttt) REVERT: 1 69 ARG cc_start: 0.8709 (mtt180) cc_final: 0.7731 (ptt180) REVERT: 1 233 MET cc_start: 0.5426 (tpt) cc_final: 0.4846 (ptm) REVERT: 3 147 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8784 (mt-10) REVERT: 3 149 MET cc_start: 0.8851 (ptm) cc_final: 0.8484 (ptm) REVERT: H 23 GLU cc_start: 0.7958 (tt0) cc_final: 0.7757 (tt0) REVERT: H 31 ASP cc_start: 0.6918 (t70) cc_final: 0.6138 (t0) REVERT: L 99 GLU cc_start: 0.8723 (tt0) cc_final: 0.8086 (tt0) REVERT: L 123 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8361 (tttp) outliers start: 3 outliers final: 0 residues processed: 81 average time/residue: 1.4562 time to fit residues: 124.6608 Evaluate side-chains 77 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 39 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.058705 restraints weight = 54210.883| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.22 r_work: 0.2706 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8569 Z= 0.110 Angle : 0.479 5.171 11671 Z= 0.251 Chirality : 0.043 0.151 1283 Planarity : 0.004 0.044 1508 Dihedral : 4.340 26.842 1185 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.11 % Allowed : 5.98 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1058 helix: -1.73 (0.62), residues: 70 sheet: 1.21 (0.28), residues: 310 loop : -0.79 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 100 TYR 0.007 0.001 TYR 2 64 PHE 0.008 0.001 PHE 2 173 TRP 0.006 0.001 TRP 1 270 HIS 0.003 0.001 HIS 1 249 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8567) covalent geometry : angle 0.47889 (11667) SS BOND : bond 0.00385 ( 2) SS BOND : angle 0.64096 ( 4) hydrogen bonds : bond 0.03245 ( 240) hydrogen bonds : angle 4.47563 ( 681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 112 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 39 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.5187 (mttt) REVERT: 1 69 ARG cc_start: 0.8730 (mtt180) cc_final: 0.7730 (ptm160) REVERT: 3 147 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8760 (mt-10) REVERT: 3 149 MET cc_start: 0.8790 (ptm) cc_final: 0.8413 (ptm) REVERT: H 16 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7944 (tpp80) REVERT: H 31 ASP cc_start: 0.6865 (t70) cc_final: 0.6035 (t0) REVERT: L 99 GLU cc_start: 0.8730 (tt0) cc_final: 0.8076 (tt0) REVERT: L 123 LYS cc_start: 0.8818 (ttpp) cc_final: 0.8361 (tttp) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 1.4461 time to fit residues: 119.3399 Evaluate side-chains 78 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 39 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.058534 restraints weight = 54215.805| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.28 r_work: 0.2712 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8569 Z= 0.093 Angle : 0.469 5.671 11671 Z= 0.245 Chirality : 0.043 0.157 1283 Planarity : 0.004 0.043 1508 Dihedral : 4.264 27.011 1185 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.44 % Allowed : 6.09 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1058 helix: -1.71 (0.62), residues: 70 sheet: 1.23 (0.28), residues: 310 loop : -0.75 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 100 TYR 0.006 0.001 TYR 2 64 PHE 0.008 0.001 PHE 2 173 TRP 0.006 0.001 TRP 1 270 HIS 0.003 0.001 HIS 1 249 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8567) covalent geometry : angle 0.46930 (11667) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.63200 ( 4) hydrogen bonds : bond 0.02991 ( 240) hydrogen bonds : angle 4.35752 ( 681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 112 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 39 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.5187 (mttt) REVERT: 1 69 ARG cc_start: 0.8719 (mtt180) cc_final: 0.7712 (ptm160) REVERT: 3 147 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8775 (mt-10) REVERT: 3 149 MET cc_start: 0.8782 (ptm) cc_final: 0.8412 (ptm) REVERT: H 16 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.8020 (tpp80) REVERT: H 23 GLU cc_start: 0.8063 (tt0) cc_final: 0.7792 (tt0) REVERT: H 31 ASP cc_start: 0.6924 (t70) cc_final: 0.5987 (t0) REVERT: H 73 ASP cc_start: 0.8288 (t0) cc_final: 0.7930 (t0) REVERT: H 76 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8682 (mtmp) REVERT: L 74 ASN cc_start: 0.8968 (p0) cc_final: 0.8765 (p0) REVERT: L 99 GLU cc_start: 0.8717 (tt0) cc_final: 0.8046 (tt0) REVERT: L 123 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8358 (tttp) outliers start: 4 outliers final: 0 residues processed: 78 average time/residue: 1.4686 time to fit residues: 121.3809 Evaluate side-chains 80 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain H residue 76 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.057791 restraints weight = 54530.121| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.29 r_work: 0.2692 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8569 Z= 0.120 Angle : 0.484 5.490 11671 Z= 0.253 Chirality : 0.043 0.153 1283 Planarity : 0.004 0.044 1508 Dihedral : 4.327 26.475 1185 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.44 % Allowed : 6.09 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1058 helix: -1.73 (0.62), residues: 70 sheet: 1.20 (0.28), residues: 310 loop : -0.77 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 100 TYR 0.007 0.001 TYR 2 64 PHE 0.009 0.001 PHE 2 173 TRP 0.006 0.001 TRP 1 270 HIS 0.004 0.001 HIS 1 249 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8567) covalent geometry : angle 0.48434 (11667) SS BOND : bond 0.00380 ( 2) SS BOND : angle 0.61777 ( 4) hydrogen bonds : bond 0.03155 ( 240) hydrogen bonds : angle 4.29676 ( 681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 112 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 39 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.5240 (mttt) REVERT: 1 69 ARG cc_start: 0.8749 (mtt180) cc_final: 0.7740 (ptm160) REVERT: 3 147 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8764 (mt-10) REVERT: 3 149 MET cc_start: 0.8778 (ptm) cc_final: 0.8414 (ptm) REVERT: H 23 GLU cc_start: 0.8106 (tt0) cc_final: 0.7864 (tt0) REVERT: H 31 ASP cc_start: 0.7009 (t70) cc_final: 0.6014 (t0) REVERT: H 73 ASP cc_start: 0.8307 (t0) cc_final: 0.7911 (t0) REVERT: H 76 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8662 (mtmp) REVERT: L 74 ASN cc_start: 0.8921 (p0) cc_final: 0.8698 (p0) REVERT: L 99 GLU cc_start: 0.8734 (tt0) cc_final: 0.8093 (tt0) REVERT: L 101 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8140 (mm-30) REVERT: L 123 LYS cc_start: 0.8842 (ttpp) cc_final: 0.8325 (tttp) outliers start: 4 outliers final: 0 residues processed: 79 average time/residue: 1.4254 time to fit residues: 119.4254 Evaluate side-chains 79 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain H residue 76 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.056966 restraints weight = 54733.690| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.27 r_work: 0.2681 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8569 Z= 0.148 Angle : 0.511 6.694 11671 Z= 0.269 Chirality : 0.044 0.154 1283 Planarity : 0.004 0.047 1508 Dihedral : 4.475 29.640 1185 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.65 % Allowed : 6.09 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.25), residues: 1058 helix: -1.67 (0.62), residues: 69 sheet: 1.16 (0.28), residues: 311 loop : -0.85 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 87 TYR 0.008 0.001 TYR 1 287 PHE 0.010 0.001 PHE 2 173 TRP 0.007 0.001 TRP 1 270 HIS 0.004 0.001 HIS 1 249 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8567) covalent geometry : angle 0.51061 (11667) SS BOND : bond 0.00383 ( 2) SS BOND : angle 0.66019 ( 4) hydrogen bonds : bond 0.03362 ( 240) hydrogen bonds : angle 4.30447 ( 681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 112 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 39 LYS cc_start: 0.6547 (OUTLIER) cc_final: 0.5233 (mttt) REVERT: 1 69 ARG cc_start: 0.8783 (mtt180) cc_final: 0.7691 (ptm160) REVERT: 3 147 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8723 (mt-10) REVERT: 3 149 MET cc_start: 0.8827 (ptm) cc_final: 0.8495 (ptm) REVERT: H 23 GLU cc_start: 0.8133 (tt0) cc_final: 0.7888 (tt0) REVERT: H 31 ASP cc_start: 0.7031 (t70) cc_final: 0.6005 (t0) REVERT: H 73 ASP cc_start: 0.8335 (t0) cc_final: 0.7959 (t0) REVERT: H 76 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8689 (mtmp) REVERT: H 89 GLU cc_start: 0.8701 (pm20) cc_final: 0.8500 (pm20) REVERT: L 74 ASN cc_start: 0.8904 (p0) cc_final: 0.8686 (p0) REVERT: L 99 GLU cc_start: 0.8735 (tt0) cc_final: 0.8142 (tt0) REVERT: L 101 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8245 (mm-30) REVERT: L 123 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8341 (tttp) outliers start: 6 outliers final: 0 residues processed: 79 average time/residue: 1.4182 time to fit residues: 118.7485 Evaluate side-chains 79 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain H residue 76 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.074674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.057763 restraints weight = 54417.146| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.28 r_work: 0.2692 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8569 Z= 0.104 Angle : 0.491 6.777 11671 Z= 0.256 Chirality : 0.043 0.155 1283 Planarity : 0.004 0.045 1508 Dihedral : 4.379 28.900 1185 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.22 % Allowed : 6.64 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.25), residues: 1058 helix: -1.72 (0.61), residues: 70 sheet: 1.24 (0.28), residues: 311 loop : -0.77 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 87 TYR 0.007 0.001 TYR 1 205 PHE 0.008 0.001 PHE 3 120 TRP 0.007 0.001 TRP 2 79 HIS 0.003 0.001 HIS 1 249 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8567) covalent geometry : angle 0.49127 (11667) SS BOND : bond 0.00387 ( 2) SS BOND : angle 0.64214 ( 4) hydrogen bonds : bond 0.03011 ( 240) hydrogen bonds : angle 4.23909 ( 681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 112 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 39 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.5212 (mttt) REVERT: 1 69 ARG cc_start: 0.8761 (mtt180) cc_final: 0.7687 (ptm160) REVERT: 3 147 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8727 (mt-10) REVERT: 3 149 MET cc_start: 0.8770 (ptm) cc_final: 0.8416 (ptm) REVERT: H 23 GLU cc_start: 0.8135 (tt0) cc_final: 0.7854 (tt0) REVERT: H 73 ASP cc_start: 0.8304 (t0) cc_final: 0.7931 (t0) REVERT: H 76 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8671 (mtmp) REVERT: H 89 GLU cc_start: 0.8676 (pm20) cc_final: 0.8467 (pm20) REVERT: L 74 ASN cc_start: 0.8866 (p0) cc_final: 0.8660 (p0) REVERT: L 99 GLU cc_start: 0.8721 (tt0) cc_final: 0.8184 (tt0) REVERT: L 101 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8241 (mm-30) REVERT: L 123 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8338 (tttp) outliers start: 2 outliers final: 0 residues processed: 77 average time/residue: 1.3796 time to fit residues: 112.5635 Evaluate side-chains 78 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain H residue 76 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.073577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.057013 restraints weight = 54597.167| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.19 r_work: 0.2670 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8569 Z= 0.164 Angle : 0.519 6.606 11671 Z= 0.273 Chirality : 0.044 0.155 1283 Planarity : 0.004 0.048 1508 Dihedral : 4.556 35.947 1185 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.22 % Allowed : 6.64 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 1058 helix: -1.71 (0.62), residues: 69 sheet: 1.13 (0.28), residues: 312 loop : -0.91 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 87 TYR 0.010 0.001 TYR 1 287 PHE 0.011 0.001 PHE 2 173 TRP 0.007 0.001 TRP 2 79 HIS 0.004 0.001 HIS 1 249 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8567) covalent geometry : angle 0.51930 (11667) SS BOND : bond 0.00388 ( 2) SS BOND : angle 0.66973 ( 4) hydrogen bonds : bond 0.03478 ( 240) hydrogen bonds : angle 4.29093 ( 681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 112 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 39 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.5305 (mttt) REVERT: 1 69 ARG cc_start: 0.8781 (mtt180) cc_final: 0.7659 (ptm160) REVERT: 3 147 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8700 (mt-10) REVERT: 3 149 MET cc_start: 0.8832 (ptm) cc_final: 0.8511 (ptm) REVERT: H 23 GLU cc_start: 0.8184 (tt0) cc_final: 0.7901 (tt0) REVERT: H 73 ASP cc_start: 0.8325 (t0) cc_final: 0.7956 (t0) REVERT: H 76 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8674 (mtmp) REVERT: H 89 GLU cc_start: 0.8730 (pm20) cc_final: 0.8512 (pm20) REVERT: L 74 ASN cc_start: 0.8866 (p0) cc_final: 0.8655 (p0) REVERT: L 99 GLU cc_start: 0.8747 (tt0) cc_final: 0.8222 (tt0) REVERT: L 101 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8232 (mm-30) REVERT: L 123 LYS cc_start: 0.8853 (ttpp) cc_final: 0.8343 (tttp) outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 1.4043 time to fit residues: 113.1234 Evaluate side-chains 77 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain H residue 76 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.074354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.057420 restraints weight = 54705.323| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.28 r_work: 0.2679 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8569 Z= 0.103 Angle : 0.488 6.661 11671 Z= 0.255 Chirality : 0.043 0.155 1283 Planarity : 0.004 0.044 1508 Dihedral : 4.445 35.579 1185 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.22 % Allowed : 6.86 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.25), residues: 1058 helix: -1.74 (0.61), residues: 70 sheet: 1.21 (0.28), residues: 311 loop : -0.81 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 87 TYR 0.006 0.001 TYR 1 205 PHE 0.008 0.001 PHE 3 120 TRP 0.007 0.001 TRP 2 79 HIS 0.003 0.001 HIS 1 249 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8567) covalent geometry : angle 0.48802 (11667) SS BOND : bond 0.00392 ( 2) SS BOND : angle 0.61757 ( 4) hydrogen bonds : bond 0.02996 ( 240) hydrogen bonds : angle 4.21576 ( 681) =============================================================================== Job complete usr+sys time: 5609.78 seconds wall clock time: 95 minutes 57.50 seconds (5757.50 seconds total)