Starting phenix.real_space_refine on Wed Aug 5 14:05:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yju_39350/08_2026/8yju_39350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yju_39350/08_2026/8yju_39350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yju_39350/08_2026/8yju_39350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yju_39350/08_2026/8yju_39350.map" model { file = "/net/cci-nas-00/data/ceres_data/8yju_39350/08_2026/8yju_39350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yju_39350/08_2026/8yju_39350.cif" } resolution = 3.78 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 361 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 61 5.16 5 C 6060 2.51 5 N 1669 2.21 5 O 2085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 9939 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "C" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1940 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 245} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2769 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "J" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 638 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 224 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 2.30, per 1000 atoms: 0.23 Number of scatterers: 9939 At special positions: 0 Unit cell: (111.22, 101.26, 108.73, 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 61 16.00 P 64 15.00 O 2085 8.00 N 1669 7.00 C 6060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 405.3 milliseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 31.2% alpha, 25.0% beta 16 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.325A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'A' and resid 8 through 20 removed outlier: 4.274A pdb=" N LEU A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.538A pdb=" N HIS A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 140 through 155 removed outlier: 3.995A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 22 through 26 removed outlier: 4.142A pdb=" N TYR D 26 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.611A pdb=" N ALA D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL D 46 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 90 through 118 removed outlier: 3.984A pdb=" N GLU D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 134 through 149 Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.661A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 242 through 254 removed outlier: 3.649A pdb=" N ALA D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 262 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 302 through 311 removed outlier: 3.601A pdb=" N LEU D 306 " --> pdb=" O ASN D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.740A pdb=" N GLY D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 344 removed outlier: 4.006A pdb=" N PHE D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.502A pdb=" N LEU B 99 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 71 removed outlier: 3.697A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 50 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 39 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 206 through 208 removed outlier: 5.167A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 112 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 59 " --> pdb=" O ARG C 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'A' and resid 66 through 71 removed outlier: 3.704A pdb=" N MET A 68 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N SER A 230 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 92 removed outlier: 3.645A pdb=" N MET A 116 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 30 removed outlier: 5.447A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 127 removed outlier: 7.206A pdb=" N GLN C 125 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS D 345 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 18 through 19 Processing sheet with id=AB2, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.605A pdb=" N ASP D 34 " --> pdb=" O ALA D 176 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2791 1.34 - 1.46: 2255 1.46 - 1.58: 4952 1.58 - 1.70: 125 1.70 - 1.82: 98 Bond restraints: 10221 Sorted by residual: bond pdb=" C3' DT J 8 " pdb=" C2' DT J 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT J 18 " pdb=" C2' DT J 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT F 17 " pdb=" C2' DT F 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.34e+00 bond pdb=" C3' DT J 6 " pdb=" C2' DT J 6 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.16e+00 bond pdb=" C1' DT J 1 " pdb=" N1 DT J 1 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 7.99e+00 ... (remaining 10216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 13667 2.64 - 5.28: 311 5.28 - 7.91: 66 7.91 - 10.55: 19 10.55 - 13.19: 4 Bond angle restraints: 14067 Sorted by residual: angle pdb=" N THR A 219 " pdb=" CA THR A 219 " pdb=" C THR A 219 " ideal model delta sigma weight residual 109.81 120.98 -11.17 2.21e+00 2.05e-01 2.55e+01 angle pdb=" C ALA A 242 " pdb=" N ASP A 243 " pdb=" CA ASP A 243 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C ALA C 231 " pdb=" N ASP C 232 " pdb=" CA ASP C 232 " ideal model delta sigma weight residual 121.54 130.46 -8.92 1.91e+00 2.74e-01 2.18e+01 angle pdb=" N THR C 219 " pdb=" CA THR C 219 " pdb=" C THR C 219 " ideal model delta sigma weight residual 109.81 119.55 -9.74 2.21e+00 2.05e-01 1.94e+01 angle pdb=" CG1 VAL D 52 " pdb=" CB VAL D 52 " pdb=" CG2 VAL D 52 " ideal model delta sigma weight residual 110.80 101.11 9.69 2.20e+00 2.07e-01 1.94e+01 ... (remaining 14062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.90: 5533 27.90 - 55.81: 574 55.81 - 83.71: 51 83.71 - 111.61: 5 111.61 - 139.51: 1 Dihedral angle restraints: 6164 sinusoidal: 2930 harmonic: 3234 Sorted by residual: dihedral pdb=" CA VAL C 7 " pdb=" C VAL C 7 " pdb=" N GLN C 8 " pdb=" CA GLN C 8 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N VAL D 52 " pdb=" CA VAL D 52 " ideal model delta harmonic sigma weight residual -180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA THR C 216 " pdb=" C THR C 216 " pdb=" N LYS C 217 " pdb=" CA LYS C 217 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 6161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1243 0.063 - 0.125: 316 0.125 - 0.188: 50 0.188 - 0.251: 7 0.251 - 0.314: 3 Chirality restraints: 1619 Sorted by residual: chirality pdb=" CA THR C 219 " pdb=" N THR C 219 " pdb=" C THR C 219 " pdb=" CB THR C 219 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB VAL D 52 " pdb=" CA VAL D 52 " pdb=" CG1 VAL D 52 " pdb=" CG2 VAL D 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.90 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA THR A 219 " pdb=" N THR A 219 " pdb=" C THR A 219 " pdb=" CB THR A 219 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1616 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 128 " 0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 129 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " 0.051 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO A 220 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 139 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO B 140 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 140 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 140 " -0.040 5.00e-02 4.00e+02 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2882 2.84 - 3.35: 8185 3.35 - 3.87: 17588 3.87 - 4.38: 19465 4.38 - 4.90: 32681 Nonbonded interactions: 80801 Sorted by model distance: nonbonded pdb=" O VAL D 123 " pdb=" OG1 THR D 127 " model vdw 2.324 3.040 nonbonded pdb=" OG1 THR D 177 " pdb=" OD1 ASP D 179 " model vdw 2.326 3.040 nonbonded pdb=" O CYS B 148 " pdb=" OG SER B 152 " model vdw 2.344 3.040 nonbonded pdb=" O ASN B 71 " pdb=" OG SER B 74 " model vdw 2.368 3.040 nonbonded pdb=" OG SER B 43 " pdb=" OH TYR B 211 " model vdw 2.368 3.040 ... (remaining 80796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB )) or resid 110 through 188 or (resid 189 and (name N or \ name CA or name C or name O or name CB )) or resid 190 through 254)) selection = (chain 'B' and (resid 2 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB )) or resid 110 through 188 or (resid 189 and (name N or \ name CA or name C or name O or name CB )) or resid 190 through 254)) selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.006 0.087 10221 Z= 0.355 Angle : 1.065 13.187 14067 Z= 0.648 Chirality : 0.059 0.314 1619 Planarity : 0.008 0.096 1589 Dihedral : 19.788 139.515 4066 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.21), residues: 1103 helix: -2.68 (0.20), residues: 318 sheet: -1.41 (0.30), residues: 280 loop : -2.39 (0.22), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 149 TYR 0.030 0.003 TYR B 249 PHE 0.024 0.003 PHE D 42 TRP 0.021 0.002 TRP D 274 HIS 0.008 0.002 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.35 (10221) covalent geometry : angle 1.06489 / 0.65 (14067) hydrogen bonds : bond 0.21497 / 14.57 ( 474) hydrogen bonds : angle 9.51251 / 6.43 ( 1306) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.7796 (p0) cc_final: 0.7540 (p0) REVERT: A 16 LEU cc_start: 0.8678 (mm) cc_final: 0.8426 (mm) REVERT: D 234 TYR cc_start: 0.8518 (m-80) cc_final: 0.8114 (m-10) REVERT: D 269 PRO cc_start: 0.8443 (Cg_endo) cc_final: 0.8188 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0797 time to fit residues: 17.6835 Evaluate side-chains 115 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN A 204 GLN C 24 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.140338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109443 restraints weight = 16358.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109812 restraints weight = 14258.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110384 restraints weight = 13619.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.110972 restraints weight = 11290.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111466 restraints weight = 10338.823| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10221 Z= 0.214 Angle : 0.692 7.206 14067 Z= 0.382 Chirality : 0.049 0.188 1619 Planarity : 0.005 0.058 1589 Dihedral : 20.899 151.533 1939 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.73 % Allowed : 9.35 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.22), residues: 1103 helix: -0.82 (0.26), residues: 323 sheet: -1.39 (0.30), residues: 293 loop : -2.09 (0.23), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 53 TYR 0.015 0.002 TYR B 239 PHE 0.014 0.002 PHE A 144 TRP 0.018 0.002 TRP D 274 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (10221) covalent geometry : angle 0.69183 / 0.38 (14067) hydrogen bonds : bond 0.05522 / 3.71 ( 474) hydrogen bonds : angle 6.67473 / 4.51 ( 1306) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.346 Fit side-chains REVERT: B 47 LEU cc_start: 0.7978 (tp) cc_final: 0.7615 (mt) REVERT: D 37 MET cc_start: 0.7807 (ttp) cc_final: 0.7525 (ttt) REVERT: D 234 TYR cc_start: 0.8599 (m-80) cc_final: 0.8104 (m-10) REVERT: D 269 PRO cc_start: 0.8522 (Cg_endo) cc_final: 0.8308 (Cg_exo) outliers start: 7 outliers final: 4 residues processed: 129 average time/residue: 0.0731 time to fit residues: 14.5530 Evaluate side-chains 109 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 116 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 28 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN C 24 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.135444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103964 restraints weight = 16902.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105183 restraints weight = 12494.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.106273 restraints weight = 10539.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.106577 restraints weight = 8448.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106786 restraints weight = 8469.631| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10221 Z= 0.189 Angle : 0.635 6.948 14067 Z= 0.347 Chirality : 0.045 0.188 1619 Planarity : 0.004 0.060 1589 Dihedral : 20.945 148.045 1939 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.14 % Allowed : 13.60 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.23), residues: 1103 helix: 0.01 (0.27), residues: 325 sheet: -1.49 (0.29), residues: 294 loop : -1.87 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 61 TYR 0.009 0.002 TYR C 250 PHE 0.016 0.002 PHE D 68 TRP 0.013 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (10221) covalent geometry : angle 0.63464 / 0.35 (14067) hydrogen bonds : bond 0.05042 / 3.35 ( 474) hydrogen bonds : angle 6.20187 / 4.22 ( 1306) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.355 Fit side-chains REVERT: B 47 LEU cc_start: 0.7978 (tp) cc_final: 0.7623 (mt) REVERT: A 139 MET cc_start: 0.8502 (ppp) cc_final: 0.8183 (ptm) REVERT: C 11 ILE cc_start: 0.7847 (mt) cc_final: 0.7588 (mt) REVERT: D 37 MET cc_start: 0.7860 (ttp) cc_final: 0.7551 (ttt) REVERT: D 65 MET cc_start: 0.6995 (mmp) cc_final: 0.6707 (mmp) REVERT: D 191 MET cc_start: 0.8758 (mtp) cc_final: 0.8541 (mtp) outliers start: 11 outliers final: 7 residues processed: 118 average time/residue: 0.0764 time to fit residues: 14.1069 Evaluate side-chains 107 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 275 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 0.9980 chunk 56 optimal weight: 0.0770 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 45 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN C 24 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.139535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108560 restraints weight = 16487.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109589 restraints weight = 14148.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110475 restraints weight = 11924.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110814 restraints weight = 10157.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.111300 restraints weight = 8892.034| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10221 Z= 0.136 Angle : 0.590 7.951 14067 Z= 0.326 Chirality : 0.044 0.185 1619 Planarity : 0.004 0.061 1589 Dihedral : 20.754 148.435 1939 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.04 % Allowed : 14.75 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.24), residues: 1103 helix: 0.51 (0.28), residues: 331 sheet: -1.31 (0.30), residues: 283 loop : -1.80 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.008 0.001 TYR B 211 PHE 0.012 0.001 PHE D 68 TRP 0.009 0.001 TRP D 274 HIS 0.004 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (10221) covalent geometry : angle 0.59006 / 0.33 (14067) hydrogen bonds : bond 0.04327 / 2.88 ( 474) hydrogen bonds : angle 5.94866 / 4.05 ( 1306) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.354 Fit side-chains REVERT: B 47 LEU cc_start: 0.7867 (tp) cc_final: 0.7591 (mt) REVERT: A 131 GLN cc_start: 0.8002 (pm20) cc_final: 0.7589 (pm20) REVERT: A 139 MET cc_start: 0.8486 (ppp) cc_final: 0.8046 (ptm) REVERT: C 11 ILE cc_start: 0.7869 (mt) cc_final: 0.7633 (mt) REVERT: D 37 MET cc_start: 0.7793 (ttp) cc_final: 0.7558 (ttt) REVERT: D 191 MET cc_start: 0.8700 (mtp) cc_final: 0.8493 (mtp) outliers start: 10 outliers final: 8 residues processed: 120 average time/residue: 0.0822 time to fit residues: 15.2064 Evaluate side-chains 113 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 275 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 0.0060 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 20 optimal weight: 0.5980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.139910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108846 restraints weight = 16375.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109030 restraints weight = 14700.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.110440 restraints weight = 13513.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110733 restraints weight = 10870.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110926 restraints weight = 10382.795| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10221 Z= 0.133 Angle : 0.581 8.059 14067 Z= 0.319 Chirality : 0.044 0.181 1619 Planarity : 0.004 0.072 1589 Dihedral : 20.726 147.373 1939 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.77 % Allowed : 16.20 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.28 (0.24), residues: 1103 helix: 0.78 (0.29), residues: 334 sheet: -1.15 (0.30), residues: 277 loop : -1.79 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 261 TYR 0.007 0.001 TYR C 133 PHE 0.018 0.001 PHE D 68 TRP 0.006 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10221) covalent geometry : angle 0.58070 / 0.32 (14067) hydrogen bonds : bond 0.04141 / 2.75 ( 474) hydrogen bonds : angle 5.75754 / 3.92 ( 1306) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.359 Fit side-chains REVERT: B 47 LEU cc_start: 0.7851 (tp) cc_final: 0.7553 (mt) REVERT: A 131 GLN cc_start: 0.8011 (pm20) cc_final: 0.7544 (pm20) REVERT: A 139 MET cc_start: 0.8426 (ppp) cc_final: 0.8020 (ptm) REVERT: C 11 ILE cc_start: 0.7890 (mt) cc_final: 0.7648 (mt) REVERT: D 191 MET cc_start: 0.8668 (mtp) cc_final: 0.8341 (mtp) REVERT: D 304 GLU cc_start: 0.6813 (pm20) cc_final: 0.6029 (tp30) outliers start: 17 outliers final: 9 residues processed: 124 average time/residue: 0.0729 time to fit residues: 14.1825 Evaluate side-chains 111 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 275 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 23 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.139388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108198 restraints weight = 16521.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108574 restraints weight = 15724.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110311 restraints weight = 13310.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.110542 restraints weight = 10638.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110845 restraints weight = 10108.421| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10221 Z= 0.142 Angle : 0.584 7.121 14067 Z= 0.318 Chirality : 0.044 0.164 1619 Planarity : 0.004 0.073 1589 Dihedral : 20.691 147.248 1939 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.87 % Allowed : 16.93 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.24), residues: 1103 helix: 0.90 (0.29), residues: 333 sheet: -1.09 (0.30), residues: 275 loop : -1.72 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 100 TYR 0.007 0.001 TYR C 239 PHE 0.020 0.001 PHE D 68 TRP 0.008 0.001 TRP D 274 HIS 0.008 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (10221) covalent geometry : angle 0.58374 / 0.32 (14067) hydrogen bonds : bond 0.04069 / 2.69 ( 474) hydrogen bonds : angle 5.62914 / 3.83 ( 1306) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.372 Fit side-chains REVERT: A 131 GLN cc_start: 0.8069 (pm20) cc_final: 0.7591 (pm20) REVERT: A 139 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8038 (ptm) REVERT: C 11 ILE cc_start: 0.7920 (mt) cc_final: 0.7673 (mt) REVERT: C 25 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7222 (mm-30) REVERT: D 141 CYS cc_start: 0.7480 (m) cc_final: 0.6907 (m) REVERT: D 160 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5915 (mt-10) REVERT: D 180 MET cc_start: 0.8578 (mmm) cc_final: 0.8140 (mpp) REVERT: D 304 GLU cc_start: 0.6824 (pm20) cc_final: 0.6198 (tp30) outliers start: 18 outliers final: 12 residues processed: 120 average time/residue: 0.0732 time to fit residues: 13.9272 Evaluate side-chains 116 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 275 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.139178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.108081 restraints weight = 16362.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108850 restraints weight = 14432.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109832 restraints weight = 12559.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110187 restraints weight = 10260.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110732 restraints weight = 9179.962| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10221 Z= 0.147 Angle : 0.598 7.243 14067 Z= 0.326 Chirality : 0.044 0.191 1619 Planarity : 0.004 0.073 1589 Dihedral : 20.695 147.026 1939 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.08 % Allowed : 17.55 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.24), residues: 1103 helix: 0.99 (0.29), residues: 333 sheet: -1.21 (0.29), residues: 282 loop : -1.69 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 61 TYR 0.007 0.001 TYR C 133 PHE 0.019 0.001 PHE D 309 TRP 0.007 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (10221) covalent geometry : angle 0.59821 / 0.33 (14067) hydrogen bonds : bond 0.04033 / 2.63 ( 474) hydrogen bonds : angle 5.59460 / 3.81 ( 1306) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.360 Fit side-chains REVERT: B 47 LEU cc_start: 0.8016 (tp) cc_final: 0.7518 (mt) REVERT: A 131 GLN cc_start: 0.8097 (pm20) cc_final: 0.7644 (pm20) REVERT: A 139 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8040 (ptm) REVERT: C 11 ILE cc_start: 0.7945 (mt) cc_final: 0.7701 (mt) REVERT: C 25 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7241 (mm-30) REVERT: D 180 MET cc_start: 0.8553 (mmm) cc_final: 0.8119 (mpp) REVERT: D 304 GLU cc_start: 0.6757 (pm20) cc_final: 0.6186 (tp30) outliers start: 20 outliers final: 10 residues processed: 120 average time/residue: 0.0690 time to fit residues: 13.4723 Evaluate side-chains 113 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 275 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.137252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.106132 restraints weight = 16196.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.106440 restraints weight = 13981.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107506 restraints weight = 13491.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.108002 restraints weight = 10615.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.108242 restraints weight = 9685.596| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10221 Z= 0.193 Angle : 0.649 11.806 14067 Z= 0.344 Chirality : 0.046 0.318 1619 Planarity : 0.004 0.078 1589 Dihedral : 20.750 146.614 1939 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.77 % Allowed : 18.28 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.24), residues: 1103 helix: 0.97 (0.29), residues: 333 sheet: -1.19 (0.29), residues: 294 loop : -1.76 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 61 TYR 0.010 0.002 TYR C 239 PHE 0.013 0.002 PHE D 68 TRP 0.006 0.001 TRP D 274 HIS 0.011 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (10221) covalent geometry : angle 0.64922 / 0.34 (14067) hydrogen bonds : bond 0.04212 / 2.73 ( 474) hydrogen bonds : angle 5.65268 / 3.84 ( 1306) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.313 Fit side-chains REVERT: A 131 GLN cc_start: 0.8150 (pm20) cc_final: 0.7707 (pm20) REVERT: A 139 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8071 (ptm) REVERT: C 25 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 68 MET cc_start: 0.8521 (pmm) cc_final: 0.8255 (pmm) REVERT: D 160 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5960 (mt-10) REVERT: D 304 GLU cc_start: 0.6808 (pm20) cc_final: 0.6220 (tp30) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 0.0781 time to fit residues: 14.7125 Evaluate side-chains 116 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 275 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 53 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.138042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106542 restraints weight = 16279.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107032 restraints weight = 14140.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107848 restraints weight = 13108.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108462 restraints weight = 11047.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110293 restraints weight = 10417.484| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10221 Z= 0.160 Angle : 0.626 9.816 14067 Z= 0.336 Chirality : 0.045 0.245 1619 Planarity : 0.004 0.077 1589 Dihedral : 20.723 146.333 1939 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.45 % Allowed : 18.69 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.24), residues: 1103 helix: 1.04 (0.29), residues: 333 sheet: -1.28 (0.28), residues: 289 loop : -1.70 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 149 TYR 0.011 0.002 TYR B 250 PHE 0.013 0.001 PHE D 68 TRP 0.006 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (10221) covalent geometry : angle 0.62573 / 0.34 (14067) hydrogen bonds : bond 0.04008 / 2.56 ( 474) hydrogen bonds : angle 5.61663 / 3.82 ( 1306) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.341 Fit side-chains REVERT: B 90 LEU cc_start: 0.8981 (mm) cc_final: 0.8644 (mp) REVERT: A 108 GLN cc_start: 0.8105 (mp10) cc_final: 0.7819 (mp10) REVERT: A 131 GLN cc_start: 0.8142 (pm20) cc_final: 0.7703 (pm20) REVERT: A 139 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8067 (ptm) REVERT: C 25 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7307 (mm-30) REVERT: D 160 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5893 (mt-10) REVERT: D 180 MET cc_start: 0.8542 (mmm) cc_final: 0.8121 (mpp) REVERT: D 304 GLU cc_start: 0.6792 (pm20) cc_final: 0.6219 (tp30) outliers start: 14 outliers final: 11 residues processed: 123 average time/residue: 0.0698 time to fit residues: 13.5856 Evaluate side-chains 119 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 95 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 56 optimal weight: 0.0000 chunk 104 optimal weight: 0.0070 chunk 79 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.139720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.108810 restraints weight = 16141.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108451 restraints weight = 13730.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109245 restraints weight = 14959.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.109874 restraints weight = 10330.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110192 restraints weight = 9641.220| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10221 Z= 0.131 Angle : 0.626 10.662 14067 Z= 0.337 Chirality : 0.045 0.273 1619 Planarity : 0.004 0.078 1589 Dihedral : 20.663 146.630 1939 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.45 % Allowed : 19.52 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.24), residues: 1103 helix: 1.07 (0.29), residues: 333 sheet: -1.26 (0.28), residues: 284 loop : -1.59 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 146 TYR 0.013 0.001 TYR D 152 PHE 0.017 0.001 PHE D 309 TRP 0.010 0.001 TRP C 28 HIS 0.003 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (10221) covalent geometry : angle 0.62558 / 0.34 (14067) hydrogen bonds : bond 0.03941 / 2.51 ( 474) hydrogen bonds : angle 5.53114 / 3.76 ( 1306) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.363 Fit side-chains REVERT: A 108 GLN cc_start: 0.8151 (mp10) cc_final: 0.7854 (mp10) REVERT: A 131 GLN cc_start: 0.8072 (pm20) cc_final: 0.7665 (pm20) REVERT: A 139 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7994 (ptm) REVERT: C 11 ILE cc_start: 0.7828 (mt) cc_final: 0.7549 (mt) REVERT: C 25 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7262 (mm-30) REVERT: C 68 MET cc_start: 0.8540 (pmm) cc_final: 0.8168 (pmm) REVERT: D 160 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5829 (mt-10) REVERT: D 180 MET cc_start: 0.8506 (mmm) cc_final: 0.8106 (mpp) REVERT: D 304 GLU cc_start: 0.6796 (pm20) cc_final: 0.5805 (tp30) outliers start: 14 outliers final: 9 residues processed: 121 average time/residue: 0.0755 time to fit residues: 14.3568 Evaluate side-chains 117 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 chunk 10 optimal weight: 0.0870 chunk 100 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.139264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108040 restraints weight = 16358.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107732 restraints weight = 13308.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108543 restraints weight = 14250.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109127 restraints weight = 9957.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109276 restraints weight = 9522.630| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10221 Z= 0.143 Angle : 0.628 9.782 14067 Z= 0.338 Chirality : 0.045 0.276 1619 Planarity : 0.004 0.074 1589 Dihedral : 20.658 146.722 1939 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.14 % Allowed : 19.52 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.24), residues: 1103 helix: 1.12 (0.29), residues: 333 sheet: -1.24 (0.28), residues: 284 loop : -1.61 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 149 TYR 0.008 0.001 TYR C 239 PHE 0.017 0.001 PHE D 309 TRP 0.014 0.001 TRP C 28 HIS 0.003 0.000 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10221) covalent geometry : angle 0.62793 / 0.34 (14067) hydrogen bonds : bond 0.03948 / 2.50 ( 474) hydrogen bonds : angle 5.48659 / 3.73 ( 1306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1553.82 seconds wall clock time: 27 minutes 46.63 seconds (1666.63 seconds total)