Starting phenix.real_space_refine on Wed Aug 5 02:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7l_72658/08_2026/9y7l_72658.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7l_72658/08_2026/9y7l_72658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y7l_72658/08_2026/9y7l_72658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7l_72658/08_2026/9y7l_72658.map" model { file = "/net/cci-nas-00/data/ceres_data/9y7l_72658/08_2026/9y7l_72658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7l_72658/08_2026/9y7l_72658.cif" } resolution = 2.7 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= 0.007 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 14 5.16 5 C 2517 2.51 5 N 714 2.21 5 O 825 1.98 5 H 3792 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7862 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1220 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 9, 'TRANS': 132} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 570 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 4, 'ARG:plan': 11, 'ASN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 7, 'GLN:plan1': 4, 'GLU:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 183 Chain: "B" Number of atoms: 3316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3316 Classifications: {'peptide': 223} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "C" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3326 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 205} Time building chain proxies: 1.17, per 1000 atoms: 0.15 Number of scatterers: 7862 At special positions: 0 Unit cell: (57.954, 70.585, 118.88, 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 14 16.00 O 825 8.00 N 714 7.00 C 2517 6.00 H 3792 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 93 " distance=2.04 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 199 " distance=2.04 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: 0.62 Conformation dependent library (CDL) restraints added in 311.9 milliseconds 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 878 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 13 sheets defined 15.2% alpha, 44.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.595A pdb=" N VAL A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 4.132A pdb=" N GLU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.663A pdb=" N GLU A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 188 through 204 removed outlier: 5.029A pdb=" N ARG A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.919A pdb=" N GLY B 198 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'C' and resid 84 through 88 removed outlier: 4.021A pdb=" N VAL C 88 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 132 removed outlier: 3.818A pdb=" N SER C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 removed outlier: 3.628A pdb=" N HIS C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 8.210A pdb=" N LEU A 160 " --> pdb=" O PRO A 58 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASN A 60 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 70 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL A 72 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N CYS A 87 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 82 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 18 " --> pdb=" O CYS A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.665A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.353A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 33 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET B 34 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.353A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 110 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.213A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.213A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.294A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.653A pdb=" N ASP C 110 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 38 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR C 54 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP C 40 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.653A pdb=" N ASP C 110 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C 102 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 119 through 123 removed outlier: 5.877A pdb=" N TYR C 178 " --> pdb=" O ASN C 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 159 211 hydrogen bonds defined for protein. 528 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: 1.29 Time building geometry restraints manager: 0.86 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: 3791 1.03 - 1.23: 24 1.23 - 1.42: 1773 1.42 - 1.62: 2339 1.62 - 1.81: 19 Bond restraints: 7946 Sorted by residual: bond pdb=" N LEU C 0 " pdb=" H1 LEU C 0 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N GLN B 1 " pdb=" H2 GLN B 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N GLN B 1 " pdb=" H3 GLN B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N GLN B 1 " pdb=" CA GLN B 1 " ideal model delta sigma weight residual 1.491 1.456 0.035 2.10e-02 2.27e+03 2.72e+00 bond pdb=" N GLN B 1 " pdb=" H1 GLN B 1 " ideal model delta sigma weight residual 0.890 0.861 0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 7941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 14055 1.85 - 3.71: 78 3.71 - 5.56: 10 5.56 - 7.41: 2 7.41 - 9.26: 1 Bond angle restraints: 14146 Sorted by residual: angle pdb=" H1 GLN B 1 " pdb=" N GLN B 1 " pdb=" H2 GLN B 1 " ideal model delta sigma weight residual 109.47 100.21 9.26 3.00e+00 1.11e-01 9.54e+00 angle pdb=" CA ARG C 147 " pdb=" CB ARG C 147 " pdb=" CG ARG C 147 " ideal model delta sigma weight residual 114.10 119.40 -5.30 2.00e+00 2.50e-01 7.02e+00 angle pdb=" CB MET C 4 " pdb=" CG MET C 4 " pdb=" SD MET C 4 " ideal model delta sigma weight residual 112.70 118.89 -6.19 3.00e+00 1.11e-01 4.26e+00 angle pdb=" CG ARG C 147 " pdb=" CD ARG C 147 " pdb=" NE ARG C 147 " ideal model delta sigma weight residual 112.00 116.40 -4.40 2.20e+00 2.07e-01 4.00e+00 angle pdb=" CA LEU C 0 " pdb=" N LEU C 0 " pdb=" H1 LEU C 0 " ideal model delta sigma weight residual 120.00 114.02 5.98 3.00e+00 1.11e-01 3.98e+00 ... (remaining 14141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3418 17.85 - 35.71: 203 35.71 - 53.56: 78 53.56 - 71.41: 17 71.41 - 89.26: 5 Dihedral angle restraints: 3721 sinusoidal: 1995 harmonic: 1726 Sorted by residual: dihedral pdb=" CA ASP C 172 " pdb=" CB ASP C 172 " pdb=" CG ASP C 172 " pdb=" OD1 ASP C 172 " ideal model delta sinusoidal sigma weight residual -30.00 -86.35 56.35 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU C 17 " pdb=" CG GLU C 17 " pdb=" CD GLU C 17 " pdb=" OE1 GLU C 17 " ideal model delta sinusoidal sigma weight residual 0.00 -89.26 89.26 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU C 84 " pdb=" CG GLU C 84 " pdb=" CD GLU C 84 " pdb=" OE1 GLU C 84 " ideal model delta sinusoidal sigma weight residual 0.00 -88.24 88.24 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 3718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 341 0.029 - 0.059: 155 0.059 - 0.088: 26 0.088 - 0.118: 43 0.118 - 0.147: 6 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA ILE C 21 " pdb=" N ILE C 21 " pdb=" C ILE C 21 " pdb=" CB ILE C 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE C 53 " pdb=" N ILE C 53 " pdb=" C ILE C 53 " pdb=" CB ILE C 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL B 150 " pdb=" N VAL B 150 " pdb=" C VAL B 150 " pdb=" CB VAL B 150 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 568 not shown) Planarity restraints: 1300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " 0.194 9.50e-02 1.11e+02 6.51e-02 5.61e+00 pdb=" NE ARG C 147 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG C 147 " -0.009 2.00e-02 2.50e+03 pdb="HH12 ARG C 147 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 147 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 147 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 216 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C ASP B 216 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP B 216 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS B 217 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 147 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C ARG C 147 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG C 147 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU C 148 " -0.010 2.00e-02 2.50e+03 ... (remaining 1297 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.44: 3958 2.44 - 2.98: 16665 2.98 - 3.52: 18312 3.52 - 4.06: 25654 4.06 - 4.60: 36456 Nonbonded interactions: 101045 Sorted by model distance: nonbonded pdb=" H GLN B 6 " pdb="HE22 GLN B 113 " model vdw 1.894 2.100 nonbonded pdb=" H GLU C 128 " pdb=" HG3 GLU C 128 " model vdw 1.906 2.270 nonbonded pdb=" HD2 ARG B 69 " pdb="HH11 ARG B 69 " model vdw 1.920 2.270 nonbonded pdb=" O ARG C 147 " pdb="HH11 ARG C 147 " model vdw 1.923 2.450 nonbonded pdb=" H SER A 108 " pdb=" HG SER A 108 " model vdw 1.937 2.100 ... (remaining 101040 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: 3.300 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: 0.030 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.210 Find NCS groups from input model: 0.020 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:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 0.035 4158 Z= 0.144 Angle : 0.517 6.193 5609 Z= 0.273 Chirality : 0.042 0.147 571 Planarity : 0.004 0.085 753 Dihedral : 13.132 89.263 1445 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.24 % Allowed : 11.86 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.59 (0.38), residues: 575 helix: 1.43 (0.75), residues: 57 sheet: 0.40 (0.35), residues: 261 loop : 0.32 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 147 TYR 0.008 0.001 TYR B 103 PHE 0.006 0.001 PHE B 50 TRP 0.021 0.001 TRP A 179 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 4154) covalent geometry : angle 0.51603 / 0.27 ( 5601) SS BOND : bond 0.00417 / 0.26 ( 4) SS BOND : angle 1.00040 / 0.81 ( 8) hydrogen bonds : bond 0.24582 / 18.91 ( 182) hydrogen bonds : angle 9.12337 / 7.01 ( 528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue ALA 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue SER 204 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: B 75 ASP cc_start: 0.8010 (t70) cc_final: 0.7770 (t70) REVERT: B 108 MET cc_start: 0.9106 (mmt) cc_final: 0.8599 (mmt) REVERT: C 17 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7644 (mp0) REVERT: C 86 GLU cc_start: 0.9219 (mp0) cc_final: 0.8937 (mp0) REVERT: C 148 GLU cc_start: 0.8286 (pt0) cc_final: 0.7642 (pp20) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.8872 time to fit residues: 38.6897 Evaluate side-chains 41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.064621 restraints weight = 21380.961| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.07 r_work: 0.2719 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4158 Z= 0.143 Angle : 0.527 5.572 5609 Z= 0.276 Chirality : 0.043 0.149 571 Planarity : 0.004 0.029 753 Dihedral : 4.186 16.379 622 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.97 % Allowed : 10.17 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.58 (0.37), residues: 575 helix: 0.93 (0.65), residues: 65 sheet: 0.70 (0.35), residues: 249 loop : 0.06 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.009 0.001 TYR B 103 PHE 0.009 0.001 PHE B 50 TRP 0.010 0.001 TRP A 179 HIS 0.001 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 4154) covalent geometry : angle 0.52530 / 0.28 ( 5601) SS BOND : bond 0.00591 / 0.36 ( 4) SS BOND : angle 1.08657 / 0.88 ( 8) hydrogen bonds : bond 0.03658 / 2.82 ( 182) hydrogen bonds : angle 6.23538 / 4.79 ( 528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue ALA 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue SER 204 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: B 75 ASP cc_start: 0.7979 (t70) cc_final: 0.7759 (t70) REVERT: B 98 CYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8152 (p) REVERT: B 108 MET cc_start: 0.9177 (mmt) cc_final: 0.8630 (mmt) REVERT: C 17 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7699 (mp0) REVERT: C 86 GLU cc_start: 0.9288 (mp0) cc_final: 0.8986 (mp0) REVERT: C 218 GLU cc_start: 0.8363 (tp30) cc_final: 0.7810 (tm-30) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.8869 time to fit residues: 40.3824 Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 212 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 50.0000 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.065322 restraints weight = 21360.577| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.08 r_work: 0.2725 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4158 Z= 0.117 Angle : 0.491 5.231 5609 Z= 0.257 Chirality : 0.043 0.143 571 Planarity : 0.003 0.038 753 Dihedral : 4.076 16.292 622 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.45 % Allowed : 9.93 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.67 (0.38), residues: 575 helix: 1.29 (0.67), residues: 65 sheet: 0.68 (0.34), residues: 262 loop : 0.08 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 147 TYR 0.008 0.001 TYR B 103 PHE 0.008 0.001 PHE B 50 TRP 0.011 0.001 TRP A 179 HIS 0.002 0.000 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 4154) covalent geometry : angle 0.49038 / 0.26 ( 5601) SS BOND : bond 0.00535 / 0.33 ( 4) SS BOND : angle 0.97596 / 0.81 ( 8) hydrogen bonds : bond 0.03208 / 2.49 ( 182) hydrogen bonds : angle 5.66012 / 4.36 ( 528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue ALA 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue SER 204 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.179 Fit side-chains REVERT: B 75 ASP cc_start: 0.8062 (t70) cc_final: 0.7650 (t70) REVERT: B 98 CYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8049 (p) REVERT: C 17 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7698 (mp0) REVERT: C 86 GLU cc_start: 0.9296 (mp0) cc_final: 0.8990 (mp0) REVERT: C 218 GLU cc_start: 0.8383 (tp30) cc_final: 0.7838 (tm-30) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.9366 time to fit residues: 43.7701 Evaluate side-chains 44 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 212 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.092106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.064942 restraints weight = 21656.351| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.09 r_work: 0.2717 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4158 Z= 0.144 Angle : 0.498 5.106 5609 Z= 0.259 Chirality : 0.043 0.142 571 Planarity : 0.004 0.049 753 Dihedral : 4.098 16.210 622 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.21 % Allowed : 10.65 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.75 (0.37), residues: 575 helix: 1.53 (0.68), residues: 65 sheet: 0.81 (0.34), residues: 260 loop : -0.01 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 147 TYR 0.008 0.001 TYR B 103 PHE 0.009 0.001 PHE B 50 TRP 0.011 0.001 TRP A 179 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.14 ( 4154) covalent geometry : angle 0.49709 / 0.26 ( 5601) SS BOND : bond 0.00538 / 0.34 ( 4) SS BOND : angle 1.10805 / 0.93 ( 8) hydrogen bonds : bond 0.03029 / 2.35 ( 182) hydrogen bonds : angle 5.40557 / 4.16 ( 528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue ALA 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue SER 204 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.136 Fit side-chains REVERT: B 75 ASP cc_start: 0.8110 (t70) cc_final: 0.7667 (t70) REVERT: B 98 CYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8108 (p) REVERT: C 17 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7714 (mp0) REVERT: C 86 GLU cc_start: 0.9307 (mp0) cc_final: 0.8998 (mp0) REVERT: C 218 GLU cc_start: 0.8433 (tp30) cc_final: 0.7835 (tm-30) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.9195 time to fit residues: 42.0919 Evaluate side-chains 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain C residue 215 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.0970 chunk 12 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 1 optimal weight: 40.0000 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.0870 chunk 54 optimal weight: 0.8980 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.065282 restraints weight = 21354.447| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.07 r_work: 0.2729 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4158 Z= 0.138 Angle : 0.490 5.081 5609 Z= 0.254 Chirality : 0.043 0.142 571 Planarity : 0.004 0.062 753 Dihedral : 4.075 16.062 622 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.21 % Allowed : 12.11 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.81 (0.37), residues: 575 helix: 1.77 (0.68), residues: 65 sheet: 0.85 (0.34), residues: 260 loop : -0.05 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 147 TYR 0.008 0.001 TYR B 103 PHE 0.009 0.001 PHE B 50 TRP 0.013 0.001 TRP A 179 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 4154) covalent geometry : angle 0.48863 / 0.25 ( 5601) SS BOND : bond 0.00528 / 0.33 ( 4) SS BOND : angle 1.10157 / 0.92 ( 8) hydrogen bonds : bond 0.02844 / 2.21 ( 182) hydrogen bonds : angle 5.16282 / 3.98 ( 528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue ALA 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue SER 204 is missing expected H atoms. Skipping. Evaluate side-chains 44 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.189 Fit side-chains REVERT: B 75 ASP cc_start: 0.8133 (t70) cc_final: 0.7657 (t70) REVERT: B 98 CYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8128 (p) REVERT: C 17 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7750 (mp0) REVERT: C 86 GLU cc_start: 0.9308 (mp0) cc_final: 0.8992 (mp0) REVERT: C 218 GLU cc_start: 0.8448 (tp30) cc_final: 0.7807 (tm-30) outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.7943 time to fit residues: 35.6628 Evaluate side-chains 41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain C residue 215 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 1 optimal weight: 40.0000 chunk 27 optimal weight: 0.3980 chunk 9 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.065954 restraints weight = 20994.957| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.08 r_work: 0.2741 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4158 Z= 0.105 Angle : 0.471 5.172 5609 Z= 0.243 Chirality : 0.042 0.139 571 Planarity : 0.004 0.068 753 Dihedral : 3.967 16.175 622 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.21 % Allowed : 11.62 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.94 (0.37), residues: 575 helix: 2.05 (0.70), residues: 65 sheet: 0.89 (0.33), residues: 260 loop : 0.03 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 147 TYR 0.008 0.001 TYR B 103 PHE 0.007 0.001 PHE B 50 TRP 0.014 0.001 TRP A 179 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.10 ( 4154) covalent geometry : angle 0.46990 / 0.24 ( 5601) SS BOND : bond 0.00470 / 0.29 ( 4) SS BOND : angle 0.96642 / 0.78 ( 8) hydrogen bonds : bond 0.02597 / 2.02 ( 182) hydrogen bonds : angle 4.91876 / 3.79 ( 528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue ALA 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue SER 204 is missing expected H atoms. Skipping. Evaluate side-chains 44 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.162 Fit side-chains REVERT: B 75 ASP cc_start: 0.8149 (t70) cc_final: 0.7673 (t70) REVERT: B 98 CYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8081 (p) REVERT: B 108 MET cc_start: 0.9144 (mmt) cc_final: 0.8587 (mmt) REVERT: C 17 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7723 (mp0) REVERT: C 86 GLU cc_start: 0.9318 (mp0) cc_final: 0.9039 (mp0) REVERT: C 218 GLU cc_start: 0.8448 (tp30) cc_final: 0.7797 (tm-30) outliers start: 5 outliers final: 2 residues processed: 44 average time/residue: 0.7722 time to fit residues: 35.4406 Evaluate side-chains 40 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 204 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 12 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.065171 restraints weight = 21436.687| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.06 r_work: 0.2724 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4158 Z= 0.147 Angle : 0.495 5.179 5609 Z= 0.256 Chirality : 0.043 0.140 571 Planarity : 0.004 0.072 753 Dihedral : 4.029 16.167 622 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.97 % Allowed : 12.59 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.92 (0.37), residues: 575 helix: 1.97 (0.70), residues: 66 sheet: 1.03 (0.34), residues: 254 loop : -0.12 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 147 TYR 0.008 0.001 TYR B 103 PHE 0.009 0.001 PHE B 50 TRP 0.015 0.001 TRP A 179 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 4154) covalent geometry : angle 0.49321 / 0.26 ( 5601) SS BOND : bond 0.00537 / 0.34 ( 4) SS BOND : angle 1.18734 / 1.00 ( 8) hydrogen bonds : bond 0.02766 / 2.14 ( 182) hydrogen bonds : angle 4.94782 / 3.81 ( 528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue ALA 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue SER 204 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.200 Fit side-chains REVERT: B 75 ASP cc_start: 0.8183 (t70) cc_final: 0.7708 (t70) REVERT: B 98 CYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 108 MET cc_start: 0.9119 (mmt) cc_final: 0.8547 (mmt) REVERT: C 17 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7765 (mp0) REVERT: C 86 GLU cc_start: 0.9308 (mp0) cc_final: 0.9027 (mp0) REVERT: C 218 GLU cc_start: 0.8428 (tp30) cc_final: 0.7743 (tm-30) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.7923 time to fit residues: 33.8833 Evaluate side-chains 41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 204 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 5 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.092196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.064953 restraints weight = 21408.572| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.08 r_work: 0.2723 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4158 Z= 0.125 Angle : 0.487 5.260 5609 Z= 0.251 Chirality : 0.043 0.140 571 Planarity : 0.004 0.078 753 Dihedral : 4.007 16.279 622 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.73 % Allowed : 13.08 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.97 (0.37), residues: 575 helix: 2.01 (0.70), residues: 66 sheet: 1.09 (0.34), residues: 253 loop : -0.13 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 147 TYR 0.008 0.001 TYR B 103 PHE 0.008 0.001 PHE B 50 TRP 0.018 0.001 TRP A 179 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4154) covalent geometry : angle 0.48564 / 0.25 ( 5601) SS BOND : bond 0.00490 / 0.31 ( 4) SS BOND : angle 1.10914 / 0.92 ( 8) hydrogen bonds : bond 0.02660 / 2.06 ( 182) hydrogen bonds : angle 4.86085 / 3.75 ( 528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue ALA 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue SER 204 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.207 Fit side-chains REVERT: B 75 ASP cc_start: 0.8228 (t70) cc_final: 0.7779 (t70) REVERT: B 98 CYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8125 (p) REVERT: B 108 MET cc_start: 0.9136 (mmt) cc_final: 0.8563 (mmt) REVERT: C 17 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7759 (mp0) REVERT: C 86 GLU cc_start: 0.9317 (mp0) cc_final: 0.9036 (mp0) REVERT: C 218 GLU cc_start: 0.8435 (tp30) cc_final: 0.7745 (tm-30) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.9308 time to fit residues: 39.7833 Evaluate side-chains 41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 204 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 40.0000 chunk 42 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.065001 restraints weight = 21333.517| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.06 r_work: 0.2721 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4158 Z= 0.147 Angle : 0.498 5.456 5609 Z= 0.257 Chirality : 0.043 0.141 571 Planarity : 0.004 0.085 753 Dihedral : 4.036 16.624 622 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.97 % Allowed : 12.83 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.98 (0.37), residues: 575 helix: 1.98 (0.70), residues: 66 sheet: 1.12 (0.34), residues: 253 loop : -0.15 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 147 TYR 0.008 0.001 TYR B 103 PHE 0.008 0.001 PHE B 50 TRP 0.020 0.001 TRP A 179 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 4154) covalent geometry : angle 0.49666 / 0.26 ( 5601) SS BOND : bond 0.00507 / 0.32 ( 4) SS BOND : angle 1.19253 / 0.99 ( 8) hydrogen bonds : bond 0.02726 / 2.11 ( 182) hydrogen bonds : angle 4.88084 / 3.76 ( 528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue ALA 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue SER 204 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.174 Fit side-chains REVERT: B 75 ASP cc_start: 0.8250 (t70) cc_final: 0.7804 (t70) REVERT: B 98 CYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8169 (p) REVERT: B 108 MET cc_start: 0.9141 (mmt) cc_final: 0.8571 (mmt) REVERT: C 17 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7767 (mp0) REVERT: C 86 GLU cc_start: 0.9323 (mp0) cc_final: 0.9045 (mp0) REVERT: C 218 GLU cc_start: 0.8442 (tp30) cc_final: 0.7733 (tm-30) outliers start: 4 outliers final: 4 residues processed: 41 average time/residue: 0.8496 time to fit residues: 36.4067 Evaluate side-chains 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 12 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.065653 restraints weight = 21300.274| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.08 r_work: 0.2739 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4158 Z= 0.093 Angle : 0.479 5.506 5609 Z= 0.246 Chirality : 0.043 0.138 571 Planarity : 0.004 0.077 753 Dihedral : 3.943 16.456 622 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.97 % Allowed : 13.32 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.09 (0.38), residues: 575 helix: 2.08 (0.70), residues: 66 sheet: 1.16 (0.34), residues: 253 loop : -0.04 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 147 TYR 0.008 0.001 TYR B 103 PHE 0.007 0.001 PHE C 103 TRP 0.021 0.001 TRP A 179 HIS 0.001 0.000 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.09 ( 4154) covalent geometry : angle 0.47783 / 0.25 ( 5601) SS BOND : bond 0.00448 / 0.28 ( 4) SS BOND : angle 0.98457 / 0.78 ( 8) hydrogen bonds : bond 0.02509 / 1.95 ( 182) hydrogen bonds : angle 4.73428 / 3.65 ( 528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue ALA 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue SER 204 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.205 Fit side-chains REVERT: B 75 ASP cc_start: 0.8217 (t70) cc_final: 0.7765 (t70) REVERT: B 98 CYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8082 (p) REVERT: B 108 MET cc_start: 0.9131 (mmt) cc_final: 0.8552 (mmt) REVERT: C 17 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7708 (mp0) REVERT: C 86 GLU cc_start: 0.9306 (mp0) cc_final: 0.9023 (mp0) REVERT: C 204 GLN cc_start: 0.8306 (mt0) cc_final: 0.7724 (mp10) REVERT: C 218 GLU cc_start: 0.8461 (tp30) cc_final: 0.7723 (tm-30) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.8305 time to fit residues: 36.4177 Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.066244 restraints weight = 20930.594| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.06 r_work: 0.2742 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4158 Z= 0.102 Angle : 0.477 5.233 5609 Z= 0.245 Chirality : 0.042 0.138 571 Planarity : 0.004 0.069 753 Dihedral : 3.900 16.163 622 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.97 % Allowed : 13.32 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.09 (0.37), residues: 575 helix: 2.14 (0.70), residues: 66 sheet: 1.15 (0.34), residues: 253 loop : -0.04 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 147 TYR 0.008 0.001 TYR B 103 PHE 0.008 0.001 PHE B 50 TRP 0.021 0.001 TRP A 179 HIS 0.001 0.000 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.10 ( 4154) covalent geometry : angle 0.47556 / 0.24 ( 5601) SS BOND : bond 0.00452 / 0.28 ( 4) SS BOND : angle 1.02028 / 0.81 ( 8) hydrogen bonds : bond 0.02495 / 1.94 ( 182) hydrogen bonds : angle 4.70665 / 3.62 ( 528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.93 seconds wall clock time: 45 minutes 16.60 seconds (2716.60 seconds total)