Starting phenix.real_space_refine on Tue Feb 3 18:28:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rxm_54366/02_2026/9rxm_54366.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rxm_54366/02_2026/9rxm_54366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rxm_54366/02_2026/9rxm_54366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rxm_54366/02_2026/9rxm_54366.map" model { file = "/net/cci-nas-00/data/ceres_data/9rxm_54366/02_2026/9rxm_54366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rxm_54366/02_2026/9rxm_54366.cif" } resolution = 3.0 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= 0.000 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3825 2.51 5 N 1052 2.21 5 O 1161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 6063 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1304 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1653 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 197} Chain breaks: 6 Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 86 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "E" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2191 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 254} Chain breaks: 1 Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Time building chain proxies: 1.25, per 1000 atoms: 0.21 Number of scatterers: 6063 At special positions: 0 Unit cell: (83.2542, 79.6027, 136.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1161 8.00 N 1052 7.00 C 3825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 89 " distance=2.02 Simple disulfide: pdb=" SG CYS B 143 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 257 " distance=2.04 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 80 " 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: 0.48 Conformation dependent library (CDL) restraints added in 258.1 milliseconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 12.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.921A pdb=" N SER B 84 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'E' and resid 54 through 83 Processing helix chain 'E' and resid 135 through 148 Processing helix chain 'E' and resid 149 through 160 Processing helix chain 'E' and resid 160 through 173 Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.606A pdb=" N TYR E 255 " --> pdb=" O GLU E 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.883A pdb=" N THR A 108 " --> pdb=" O GLN A 10 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP A 33 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 55 removed outlier: 5.526A pdb=" N GLN B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B 48 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 54 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B 41 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR B 36 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE B 43 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN B 34 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 45 " --> pdb=" O TRP B 32 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 86 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 55 removed outlier: 5.526A pdb=" N GLN B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B 48 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 54 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B 41 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR B 36 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE B 43 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN B 34 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 45 " --> pdb=" O TRP B 32 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 86 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.989A pdb=" N VAL B 142 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 148 removed outlier: 4.862A pdb=" N THR B 146 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 188 " --> pdb=" O THR B 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 212 Processing sheet with id=AB2, first strand: chain 'E' and resid 44 through 45 removed outlier: 5.164A pdb=" N GLN E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL E 26 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL E 32 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS E 99 " --> pdb=" O MET E 3 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 109 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR E 116 " --> pdb=" O ASP E 120 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 188 through 191 removed outlier: 3.924A pdb=" N HIS E 190 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR E 198 " --> pdb=" O HIS E 190 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU E 199 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL E 245 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS E 201 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA E 243 " --> pdb=" O CYS E 201 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS E 241 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 205 " --> pdb=" O PHE E 239 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE E 239 " --> pdb=" O GLY E 205 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA E 244 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 227 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 188 through 191 removed outlier: 3.924A pdb=" N HIS E 190 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR E 198 " --> pdb=" O HIS E 190 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU E 199 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL E 245 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS E 201 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA E 243 " --> pdb=" O CYS E 201 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS E 241 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 205 " --> pdb=" O PHE E 239 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE E 239 " --> pdb=" O GLY E 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AB6, first strand: chain 'F' and resid 8 through 11 removed outlier: 5.692A pdb=" N PHE F 62 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER F 55 " --> pdb=" O TYR F 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 36 through 41 198 hydrogen bonds defined for protein. 492 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: 0.73 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1990 1.34 - 1.46: 1492 1.46 - 1.58: 2694 1.58 - 1.70: 0 1.70 - 1.81: 35 Bond restraints: 6211 Sorted by residual: bond pdb=" CA GLU A 14 " pdb=" C GLU A 14 " ideal model delta sigma weight residual 1.522 1.558 -0.036 1.72e-02 3.38e+03 4.48e+00 bond pdb=" CB MET E 43 " pdb=" CG MET E 43 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CA ILE A 6 " pdb=" C ILE A 6 " ideal model delta sigma weight residual 1.520 1.530 -0.010 8.80e-03 1.29e+04 1.32e+00 bond pdb=" SD MET E 65 " pdb=" CE MET E 65 " ideal model delta sigma weight residual 1.791 1.764 0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CA ILE A 6 " pdb=" CB ILE A 6 " ideal model delta sigma weight residual 1.534 1.542 -0.007 6.80e-03 2.16e+04 1.13e+00 ... (remaining 6206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 8255 2.32 - 4.63: 138 4.63 - 6.95: 9 6.95 - 9.27: 2 9.27 - 11.59: 1 Bond angle restraints: 8405 Sorted by residual: angle pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" C GLU A 16 " ideal model delta sigma weight residual 107.73 113.35 -5.62 1.34e+00 5.57e-01 1.76e+01 angle pdb=" C GLN A 5 " pdb=" N ILE A 6 " pdb=" CA ILE A 6 " ideal model delta sigma weight residual 120.24 122.71 -2.47 6.30e-01 2.52e+00 1.54e+01 angle pdb=" N TRP B 157 " pdb=" CA TRP B 157 " pdb=" C TRP B 157 " ideal model delta sigma weight residual 110.91 115.20 -4.29 1.17e+00 7.31e-01 1.34e+01 angle pdb=" N ASP A 17 " pdb=" CA ASP A 17 " pdb=" C ASP A 17 " ideal model delta sigma weight residual 110.91 115.08 -4.17 1.17e+00 7.31e-01 1.27e+01 angle pdb=" CA LEU F 23 " pdb=" CB LEU F 23 " pdb=" CG LEU F 23 " ideal model delta sigma weight residual 116.30 127.89 -11.59 3.50e+00 8.16e-02 1.10e+01 ... (remaining 8400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 3294 16.68 - 33.36: 289 33.36 - 50.04: 69 50.04 - 66.71: 19 66.71 - 83.39: 7 Dihedral angle restraints: 3678 sinusoidal: 1506 harmonic: 2172 Sorted by residual: dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 257 " pdb=" CB CYS E 257 " ideal model delta sinusoidal sigma weight residual 93.00 157.41 -64.41 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 88 " pdb=" CB CYS A 88 " ideal model delta sinusoidal sigma weight residual 93.00 152.41 -59.41 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CA MET E 65 " pdb=" C MET E 65 " pdb=" N LYS E 66 " pdb=" CA LYS E 66 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 3675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 680 0.046 - 0.092: 159 0.092 - 0.138: 36 0.138 - 0.183: 7 0.183 - 0.229: 2 Chirality restraints: 884 Sorted by residual: chirality pdb=" CA MET E 65 " pdb=" N MET E 65 " pdb=" C MET E 65 " pdb=" CB MET E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CG LEU F 23 " pdb=" CB LEU F 23 " pdb=" CD1 LEU F 23 " pdb=" CD2 LEU F 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE B 10 " pdb=" CA ILE B 10 " pdb=" CG1 ILE B 10 " pdb=" CG2 ILE B 10 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 881 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 110 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 111 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 70 " 0.010 2.00e-02 2.50e+03 1.40e-02 3.43e+00 pdb=" CG PHE F 70 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE F 70 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 70 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 70 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 70 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE F 70 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 65 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C MET E 65 " -0.032 2.00e-02 2.50e+03 pdb=" O MET E 65 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS E 66 " 0.011 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 315 2.72 - 3.26: 6390 3.26 - 3.81: 10577 3.81 - 4.35: 13363 4.35 - 4.90: 22144 Nonbonded interactions: 52789 Sorted by model distance: nonbonded pdb=" OG SER F 11 " pdb=" OD1 ASN F 21 " model vdw 2.169 3.040 nonbonded pdb=" OG SER F 88 " pdb=" OE1 GLN F 89 " model vdw 2.184 3.040 nonbonded pdb=" NH1 ARG E 109 " pdb=" O GLY E 110 " model vdw 2.196 3.120 nonbonded pdb=" O LYS E 66 " pdb=" NE2 GLN E 70 " model vdw 2.233 3.120 nonbonded pdb=" O PRO E 233 " pdb=" OH TYR F 10 " model vdw 2.234 3.040 ... (remaining 52784 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: 1.280 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.120 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 0.040 6217 Z= 0.163 Angle : 0.698 11.586 8417 Z= 0.379 Chirality : 0.044 0.229 884 Planarity : 0.005 0.112 1092 Dihedral : 13.989 83.392 2258 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.20 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.41 (0.30), residues: 716 helix: -0.15 (0.54), residues: 78 sheet: -1.09 (0.40), residues: 185 loop : -2.21 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 73 TYR 0.014 0.002 TYR B 47 PHE 0.031 0.002 PHE F 70 TRP 0.023 0.002 TRP A 176 HIS 0.002 0.000 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6211) covalent geometry : angle 0.69655 ( 8405) SS BOND : bond 0.00365 ( 6) SS BOND : angle 1.29301 ( 12) hydrogen bonds : bond 0.27627 ( 182) hydrogen bonds : angle 10.86470 ( 492) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 21 TYR cc_start: 0.6575 (t80) cc_final: 0.5983 (t80) REVERT: A 140 ASP cc_start: 0.8491 (t70) cc_final: 0.8269 (t70) REVERT: A 160 VAL cc_start: 0.8677 (m) cc_final: 0.8314 (m) REVERT: B 11 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7323 (mtpp) REVERT: B 114 ASP cc_start: 0.8672 (t0) cc_final: 0.8151 (t70) REVERT: B 116 LYS cc_start: 0.9024 (ptpp) cc_final: 0.8573 (ptpp) REVERT: B 211 GLN cc_start: 0.7921 (mp10) cc_final: 0.7578 (mp10) REVERT: E 129 ARG cc_start: 0.8002 (mpt180) cc_final: 0.7750 (mpt180) REVERT: F 6 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7585 (mttp) REVERT: F 24 ASN cc_start: 0.6758 (m110) cc_final: 0.6472 (m110) REVERT: F 41 LYS cc_start: 0.7666 (mppt) cc_final: 0.7057 (mptt) REVERT: F 48 LYS cc_start: 0.8432 (mppt) cc_final: 0.8231 (mppt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.4241 time to fit residues: 57.2417 Evaluate side-chains 100 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.0040 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 HIS E 52 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.144468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.119440 restraints weight = 11581.092| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.47 r_work: 0.4050 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6217 Z= 0.158 Angle : 0.693 8.624 8417 Z= 0.359 Chirality : 0.044 0.221 884 Planarity : 0.005 0.077 1092 Dihedral : 5.229 24.961 816 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.64 % Favored : 90.22 % Rotamer: Outliers : 1.37 % Allowed : 12.59 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.35 (0.30), residues: 716 helix: 0.32 (0.56), residues: 76 sheet: -1.37 (0.39), residues: 189 loop : -2.08 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 254 TYR 0.022 0.002 TYR B 47 PHE 0.017 0.002 PHE B 119 TRP 0.018 0.001 TRP E 202 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6211) covalent geometry : angle 0.69245 ( 8405) SS BOND : bond 0.00431 ( 6) SS BOND : angle 1.12267 ( 12) hydrogen bonds : bond 0.04847 ( 182) hydrogen bonds : angle 7.23703 ( 492) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.6799 (t80) cc_final: 0.6352 (t80) REVERT: A 82 ASP cc_start: 0.8145 (m-30) cc_final: 0.7772 (m-30) REVERT: A 140 ASP cc_start: 0.8767 (t70) cc_final: 0.8492 (t70) REVERT: B 11 LYS cc_start: 0.7904 (mtpp) cc_final: 0.7329 (mtpp) REVERT: B 114 ASP cc_start: 0.8819 (t0) cc_final: 0.8521 (t70) REVERT: B 116 LYS cc_start: 0.9242 (ptpp) cc_final: 0.8732 (ptpp) REVERT: B 157 TRP cc_start: 0.7625 (m100) cc_final: 0.7425 (m100) REVERT: F 6 LYS cc_start: 0.7941 (mtmm) cc_final: 0.7483 (mttp) REVERT: F 24 ASN cc_start: 0.7333 (m110) cc_final: 0.7080 (m110) REVERT: F 48 LYS cc_start: 0.8561 (mppt) cc_final: 0.8271 (mppt) REVERT: F 58 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8343 (tptm) outliers start: 9 outliers final: 4 residues processed: 120 average time/residue: 0.3472 time to fit residues: 44.3491 Evaluate side-chains 99 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 58 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN E 60 GLN E 64 ASN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN F 51 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.140330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.115214 restraints weight = 11376.116| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.40 r_work: 0.3992 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6217 Z= 0.200 Angle : 0.696 10.254 8417 Z= 0.358 Chirality : 0.044 0.183 884 Planarity : 0.004 0.064 1092 Dihedral : 5.250 22.984 816 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.75 % Favored : 89.11 % Rotamer: Outliers : 1.82 % Allowed : 16.24 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.33 (0.30), residues: 716 helix: 0.56 (0.56), residues: 70 sheet: -1.60 (0.38), residues: 201 loop : -1.93 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 254 TYR 0.019 0.002 TYR E 97 PHE 0.015 0.002 PHE A 18 TRP 0.015 0.001 TRP E 202 HIS 0.003 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 6211) covalent geometry : angle 0.69477 ( 8405) SS BOND : bond 0.00519 ( 6) SS BOND : angle 1.28758 ( 12) hydrogen bonds : bond 0.04809 ( 182) hydrogen bonds : angle 6.84407 ( 492) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.6986 (t80) cc_final: 0.6394 (t80) REVERT: A 68 LYS cc_start: 0.8263 (mptt) cc_final: 0.7890 (ttpt) REVERT: A 82 ASP cc_start: 0.8059 (m-30) cc_final: 0.7606 (m-30) REVERT: A 92 ARG cc_start: 0.8139 (tmm160) cc_final: 0.7938 (tmm160) REVERT: A 140 ASP cc_start: 0.8806 (t70) cc_final: 0.8521 (t70) REVERT: B 11 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7381 (mtpp) REVERT: B 116 LYS cc_start: 0.9246 (ptpp) cc_final: 0.8805 (ptpp) REVERT: B 157 TRP cc_start: 0.7714 (m100) cc_final: 0.7071 (m100) REVERT: B 158 TRP cc_start: 0.8280 (m100) cc_final: 0.7747 (m100) REVERT: E 43 MET cc_start: 0.7141 (tpt) cc_final: 0.6666 (tpt) REVERT: E 174 LYS cc_start: 0.8814 (mmtm) cc_final: 0.8574 (mmtm) REVERT: F 8 GLN cc_start: 0.7112 (mt0) cc_final: 0.6808 (mt0) REVERT: F 48 LYS cc_start: 0.8484 (mppt) cc_final: 0.8178 (mppt) outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 0.3286 time to fit residues: 41.8843 Evaluate side-chains 103 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 117 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.143188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.118329 restraints weight = 11546.128| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 3.42 r_work: 0.4041 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6217 Z= 0.154 Angle : 0.678 10.136 8417 Z= 0.346 Chirality : 0.043 0.227 884 Planarity : 0.004 0.059 1092 Dihedral : 5.072 21.249 816 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.34 % Favored : 89.53 % Rotamer: Outliers : 2.43 % Allowed : 19.12 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.44 (0.29), residues: 716 helix: 0.21 (0.56), residues: 76 sheet: -1.53 (0.37), residues: 200 loop : -2.07 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 53 TYR 0.016 0.002 TYR E 97 PHE 0.018 0.002 PHE B 119 TRP 0.016 0.001 TRP E 202 HIS 0.005 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6211) covalent geometry : angle 0.67738 ( 8405) SS BOND : bond 0.00398 ( 6) SS BOND : angle 1.17069 ( 12) hydrogen bonds : bond 0.04275 ( 182) hydrogen bonds : angle 6.43802 ( 492) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.6835 (t80) cc_final: 0.6294 (t80) REVERT: A 68 LYS cc_start: 0.8236 (mptt) cc_final: 0.7886 (ttpt) REVERT: A 82 ASP cc_start: 0.8134 (m-30) cc_final: 0.7731 (m-30) REVERT: A 140 ASP cc_start: 0.8767 (t70) cc_final: 0.8478 (t70) REVERT: B 11 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7493 (mtpp) REVERT: B 114 ASP cc_start: 0.8655 (t0) cc_final: 0.8171 (t0) REVERT: B 116 LYS cc_start: 0.9115 (ptpp) cc_final: 0.8683 (ptpp) REVERT: B 157 TRP cc_start: 0.7609 (m100) cc_final: 0.6982 (m100) REVERT: B 158 TRP cc_start: 0.8268 (m100) cc_final: 0.7714 (m100) REVERT: E 174 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8558 (mmtm) REVERT: F 6 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7469 (mttp) REVERT: F 48 LYS cc_start: 0.8516 (mppt) cc_final: 0.8205 (mppt) REVERT: F 58 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8472 (tptm) REVERT: F 77 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7458 (tm-30) outliers start: 16 outliers final: 7 residues processed: 119 average time/residue: 0.3456 time to fit residues: 43.9027 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 92 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 31 optimal weight: 0.0170 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 0.0980 chunk 46 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 117 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.138221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.112835 restraints weight = 11755.745| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 3.35 r_work: 0.3953 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6217 Z= 0.231 Angle : 0.714 10.536 8417 Z= 0.368 Chirality : 0.044 0.239 884 Planarity : 0.004 0.055 1092 Dihedral : 5.313 21.800 816 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.17 % Favored : 88.69 % Rotamer: Outliers : 3.19 % Allowed : 19.58 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.42 (0.29), residues: 716 helix: 0.47 (0.58), residues: 70 sheet: -1.58 (0.37), residues: 201 loop : -2.04 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 53 TYR 0.019 0.002 TYR E 97 PHE 0.015 0.002 PHE A 18 TRP 0.015 0.001 TRP E 202 HIS 0.006 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 6211) covalent geometry : angle 0.71205 ( 8405) SS BOND : bond 0.00646 ( 6) SS BOND : angle 1.47960 ( 12) hydrogen bonds : bond 0.04690 ( 182) hydrogen bonds : angle 6.59805 ( 492) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.7038 (t80) cc_final: 0.6452 (t80) REVERT: A 82 ASP cc_start: 0.8154 (m-30) cc_final: 0.7757 (m-30) REVERT: A 140 ASP cc_start: 0.8795 (t70) cc_final: 0.8503 (t70) REVERT: B 11 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7422 (mtpp) REVERT: B 114 ASP cc_start: 0.8653 (t0) cc_final: 0.8083 (t0) REVERT: B 116 LYS cc_start: 0.9113 (ptpp) cc_final: 0.8571 (ptpp) REVERT: B 157 TRP cc_start: 0.7744 (m100) cc_final: 0.7110 (m100) REVERT: B 158 TRP cc_start: 0.8322 (m100) cc_final: 0.7753 (m100) REVERT: E 43 MET cc_start: 0.7096 (tpt) cc_final: 0.6646 (tpt) REVERT: E 174 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8616 (mmtm) REVERT: F 48 LYS cc_start: 0.8474 (mppt) cc_final: 0.8182 (mppt) outliers start: 21 outliers final: 9 residues processed: 109 average time/residue: 0.3231 time to fit residues: 37.7859 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 92 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.142347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.117190 restraints weight = 11544.055| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 3.44 r_work: 0.4027 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6217 Z= 0.157 Angle : 0.668 9.519 8417 Z= 0.343 Chirality : 0.043 0.254 884 Planarity : 0.004 0.055 1092 Dihedral : 5.103 21.241 816 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.31 % Favored : 88.55 % Rotamer: Outliers : 2.43 % Allowed : 22.31 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.57 (0.29), residues: 716 helix: 0.27 (0.56), residues: 76 sheet: -1.78 (0.36), residues: 209 loop : -2.09 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 53 TYR 0.016 0.002 TYR B 47 PHE 0.019 0.002 PHE B 119 TRP 0.027 0.001 TRP A 176 HIS 0.002 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6211) covalent geometry : angle 0.66699 ( 8405) SS BOND : bond 0.00363 ( 6) SS BOND : angle 1.28489 ( 12) hydrogen bonds : bond 0.04130 ( 182) hydrogen bonds : angle 6.37032 ( 492) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8774 (t70) cc_final: 0.8484 (t70) REVERT: B 11 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7379 (mtpp) REVERT: B 114 ASP cc_start: 0.8600 (t0) cc_final: 0.8015 (t0) REVERT: B 116 LYS cc_start: 0.9120 (ptpp) cc_final: 0.8572 (ptpp) REVERT: B 157 TRP cc_start: 0.7485 (m100) cc_final: 0.6800 (m100) REVERT: B 158 TRP cc_start: 0.8240 (m100) cc_final: 0.7565 (m100) REVERT: E 43 MET cc_start: 0.6812 (tpt) cc_final: 0.6592 (tpt) REVERT: E 174 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8609 (mmtm) REVERT: F 6 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7554 (mttp) REVERT: F 8 GLN cc_start: 0.7274 (mt0) cc_final: 0.7043 (mt0) REVERT: F 48 LYS cc_start: 0.8525 (mppt) cc_final: 0.8204 (mppt) outliers start: 16 outliers final: 10 residues processed: 119 average time/residue: 0.3260 time to fit residues: 41.4004 Evaluate side-chains 107 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 92 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 6.9990 chunk 21 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 chunk 71 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 117 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.143747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.119061 restraints weight = 11602.050| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.45 r_work: 0.4061 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6217 Z= 0.145 Angle : 0.672 10.752 8417 Z= 0.342 Chirality : 0.043 0.268 884 Planarity : 0.004 0.050 1092 Dihedral : 5.052 20.710 816 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.61 % Favored : 89.25 % Rotamer: Outliers : 1.82 % Allowed : 23.82 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.53 (0.29), residues: 716 helix: 0.39 (0.57), residues: 76 sheet: -1.73 (0.35), residues: 209 loop : -2.10 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 4 TYR 0.017 0.002 TYR E 25 PHE 0.014 0.002 PHE E 31 TRP 0.016 0.001 TRP E 202 HIS 0.004 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6211) covalent geometry : angle 0.67001 ( 8405) SS BOND : bond 0.00352 ( 6) SS BOND : angle 1.44100 ( 12) hydrogen bonds : bond 0.03982 ( 182) hydrogen bonds : angle 6.17285 ( 492) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8263 (mptt) cc_final: 0.8005 (tttt) REVERT: A 140 ASP cc_start: 0.8725 (t70) cc_final: 0.8443 (t70) REVERT: B 114 ASP cc_start: 0.8589 (t0) cc_final: 0.7920 (t0) REVERT: B 116 LYS cc_start: 0.9108 (ptpp) cc_final: 0.8557 (ptpp) REVERT: B 158 TRP cc_start: 0.8170 (m100) cc_final: 0.7499 (m100) REVERT: E 174 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8542 (mmtm) REVERT: F 6 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7425 (mttp) REVERT: F 16 GLU cc_start: 0.7505 (pm20) cc_final: 0.7097 (tm-30) REVERT: F 48 LYS cc_start: 0.8547 (mppt) cc_final: 0.8226 (mppt) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.4115 time to fit residues: 46.9204 Evaluate side-chains 100 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 92 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.138673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.113306 restraints weight = 11663.448| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.43 r_work: 0.3964 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6217 Z= 0.224 Angle : 0.727 10.021 8417 Z= 0.371 Chirality : 0.044 0.268 884 Planarity : 0.005 0.065 1092 Dihedral : 5.270 20.901 816 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.73 % Favored : 88.13 % Rotamer: Outliers : 3.64 % Allowed : 23.37 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.51 (0.30), residues: 716 helix: 0.63 (0.58), residues: 70 sheet: -1.81 (0.36), residues: 209 loop : -2.05 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 4 TYR 0.021 0.002 TYR A 34 PHE 0.018 0.002 PHE B 119 TRP 0.023 0.002 TRP E 215 HIS 0.003 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 6211) covalent geometry : angle 0.72592 ( 8405) SS BOND : bond 0.00495 ( 6) SS BOND : angle 1.42716 ( 12) hydrogen bonds : bond 0.04405 ( 182) hydrogen bonds : angle 6.42808 ( 492) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8787 (t70) cc_final: 0.8491 (t70) REVERT: B 114 ASP cc_start: 0.8636 (t0) cc_final: 0.8015 (t0) REVERT: B 116 LYS cc_start: 0.9132 (ptpp) cc_final: 0.8600 (ptpp) REVERT: B 126 PHE cc_start: 0.5503 (m-80) cc_final: 0.5189 (m-80) REVERT: B 158 TRP cc_start: 0.8198 (m100) cc_final: 0.7567 (m100) REVERT: F 16 GLU cc_start: 0.7470 (pm20) cc_final: 0.7040 (tm-30) REVERT: F 48 LYS cc_start: 0.8577 (mppt) cc_final: 0.8264 (mppt) outliers start: 24 outliers final: 12 residues processed: 108 average time/residue: 0.3706 time to fit residues: 42.7859 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 92 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.141616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.116822 restraints weight = 11677.520| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 3.40 r_work: 0.4017 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6217 Z= 0.168 Angle : 0.713 11.039 8417 Z= 0.363 Chirality : 0.044 0.292 884 Planarity : 0.004 0.047 1092 Dihedral : 5.211 21.257 816 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.31 % Favored : 88.55 % Rotamer: Outliers : 2.43 % Allowed : 24.28 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.47 (0.30), residues: 716 helix: 0.66 (0.58), residues: 70 sheet: -1.72 (0.37), residues: 200 loop : -2.07 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.020 0.002 TYR A 34 PHE 0.014 0.002 PHE A 18 TRP 0.020 0.001 TRP E 215 HIS 0.006 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6211) covalent geometry : angle 0.71021 ( 8405) SS BOND : bond 0.00386 ( 6) SS BOND : angle 1.72156 ( 12) hydrogen bonds : bond 0.04102 ( 182) hydrogen bonds : angle 6.34604 ( 492) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8739 (t70) cc_final: 0.8455 (t70) REVERT: B 114 ASP cc_start: 0.8593 (t0) cc_final: 0.7946 (t0) REVERT: B 116 LYS cc_start: 0.9103 (ptpp) cc_final: 0.8550 (ptpp) REVERT: B 126 PHE cc_start: 0.5374 (m-80) cc_final: 0.5071 (m-80) REVERT: B 158 TRP cc_start: 0.8183 (m100) cc_final: 0.7551 (m100) REVERT: E 174 LYS cc_start: 0.8678 (mmtp) cc_final: 0.8468 (mmtm) REVERT: E 241 LYS cc_start: 0.7481 (tppp) cc_final: 0.6951 (tptm) REVERT: F 6 LYS cc_start: 0.7903 (mtmm) cc_final: 0.7513 (mttp) REVERT: F 16 GLU cc_start: 0.7448 (pm20) cc_final: 0.7052 (tm-30) REVERT: F 48 LYS cc_start: 0.8618 (mppt) cc_final: 0.8288 (mppt) outliers start: 16 outliers final: 10 residues processed: 106 average time/residue: 0.3813 time to fit residues: 43.2587 Evaluate side-chains 101 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN E 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.142092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.117096 restraints weight = 11684.119| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 3.52 r_work: 0.4018 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6217 Z= 0.168 Angle : 0.736 14.741 8417 Z= 0.368 Chirality : 0.046 0.299 884 Planarity : 0.004 0.046 1092 Dihedral : 5.176 21.417 816 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.59 % Favored : 88.27 % Rotamer: Outliers : 1.97 % Allowed : 24.73 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.56 (0.30), residues: 716 helix: 0.39 (0.56), residues: 70 sheet: -1.81 (0.36), residues: 209 loop : -2.06 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 73 TYR 0.022 0.002 TYR E 25 PHE 0.019 0.002 PHE B 119 TRP 0.019 0.001 TRP A 176 HIS 0.002 0.000 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6211) covalent geometry : angle 0.73453 ( 8405) SS BOND : bond 0.00391 ( 6) SS BOND : angle 1.42439 ( 12) hydrogen bonds : bond 0.04141 ( 182) hydrogen bonds : angle 6.38941 ( 492) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8756 (t70) cc_final: 0.8456 (t70) REVERT: B 114 ASP cc_start: 0.8567 (t0) cc_final: 0.7924 (t0) REVERT: B 116 LYS cc_start: 0.9074 (ptpp) cc_final: 0.8521 (ptpp) REVERT: B 158 TRP cc_start: 0.8213 (m100) cc_final: 0.7596 (m100) REVERT: E 241 LYS cc_start: 0.7444 (tppp) cc_final: 0.6972 (tptm) REVERT: F 6 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7516 (mttp) REVERT: F 16 GLU cc_start: 0.7424 (pm20) cc_final: 0.7008 (tm-30) REVERT: F 36 GLU cc_start: 0.7368 (tp30) cc_final: 0.6986 (tm-30) REVERT: F 48 LYS cc_start: 0.8616 (mppt) cc_final: 0.8272 (mppt) outliers start: 13 outliers final: 12 residues processed: 103 average time/residue: 0.3707 time to fit residues: 40.9908 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 0.0030 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.2980 chunk 63 optimal weight: 0.0070 chunk 67 optimal weight: 0.0370 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 overall best weight: 0.2486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.148430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.124078 restraints weight = 11692.000| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 3.55 r_work: 0.4130 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6217 Z= 0.131 Angle : 0.724 12.655 8417 Z= 0.360 Chirality : 0.045 0.302 884 Planarity : 0.004 0.044 1092 Dihedral : 5.016 21.823 816 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.06 % Favored : 89.80 % Rotamer: Outliers : 1.67 % Allowed : 25.49 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: -2.54 (0.29), residues: 716 helix: 0.08 (0.54), residues: 76 sheet: -1.62 (0.36), residues: 200 loop : -2.12 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 73 TYR 0.019 0.002 TYR E 25 PHE 0.014 0.002 PHE A 18 TRP 0.020 0.002 TRP E 215 HIS 0.005 0.001 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6211) covalent geometry : angle 0.72386 ( 8405) SS BOND : bond 0.00339 ( 6) SS BOND : angle 1.01928 ( 12) hydrogen bonds : bond 0.03807 ( 182) hydrogen bonds : angle 6.20052 ( 492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.62 seconds wall clock time: 39 minutes 38.05 seconds (2378.05 seconds total)