Starting phenix.real_space_refine on Thu Jul 2 20:33:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yju_39350/07_2026/8yju_39350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yju_39350/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yju_39350/07_2026/8yju_39350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yju_39350/07_2026/8yju_39350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yju_39350/07_2026/8yju_39350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yju_39350/07_2026/8yju_39350.map" } 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-dev-6108/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: 2.45, per 1000 atoms: 0.25 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: 0.95 Conformation dependent library (CDL) restraints added in 317.1 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: 1.15 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: 1.73 Time building geometry restraints manager: 1.25 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: 3.570 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.580 Find NCS groups from input model: 0.140 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- 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 : 1.064 13.187 14067 Z= 0.646 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 1.06391 / 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 : 0.364 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: 0.0850 time to fit residues: 18.7124 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 : 0.379 ------------------------------------------------------------------------------- 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 = 0.140287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.109220 restraints weight = 16330.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.109408 restraints weight = 15568.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110548 restraints weight = 13486.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110951 restraints weight = 10693.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111491 restraints weight = 10311.745| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10221 Z= 0.214 Angle : 0.691 7.322 14067 Z= 0.381 Chirality : 0.048 0.177 1619 Planarity : 0.005 0.060 1589 Dihedral : 20.946 151.770 1939 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.73 % Allowed : 9.45 % Favored : 89.82 % 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: -2.37 (0.22), residues: 1103 helix: -0.89 (0.26), residues: 324 sheet: -1.38 (0.30), residues: 293 loop : -2.09 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 149 TYR 0.015 0.002 TYR B 239 PHE 0.015 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 0.00460 / 0.21 (10221) covalent geometry : angle 0.69148 / 0.38 (14067) hydrogen bonds : bond 0.05765 / 3.88 ( 474) hydrogen bonds : angle 6.66938 / 4.50 ( 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 134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.355 Fit side-chains REVERT: B 47 LEU cc_start: 0.7948 (tp) cc_final: 0.7619 (mt) REVERT: D 37 MET cc_start: 0.7847 (ttp) cc_final: 0.7564 (ttt) REVERT: D 234 TYR cc_start: 0.8592 (m-80) cc_final: 0.8106 (m-10) REVERT: D 269 PRO cc_start: 0.8531 (Cg_endo) cc_final: 0.8319 (Cg_exo) outliers start: 7 outliers final: 4 residues processed: 129 average time/residue: 0.0771 time to fit residues: 15.4171 Evaluate side-chains 110 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.136862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.105336 restraints weight = 16885.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.105845 restraints weight = 13314.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106861 restraints weight = 12101.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107252 restraints weight = 9950.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107449 restraints weight = 9174.109| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10221 Z= 0.158 Angle : 0.608 6.905 14067 Z= 0.336 Chirality : 0.045 0.180 1619 Planarity : 0.004 0.063 1589 Dihedral : 20.927 149.404 1939 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.83 % Allowed : 13.40 % Favored : 85.77 % 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: -0.05 (0.27), residues: 325 sheet: -1.37 (0.29), residues: 291 loop : -1.90 (0.24), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 61 TYR 0.008 0.001 TYR B 239 PHE 0.017 0.001 PHE D 68 TRP 0.012 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (10221) covalent geometry : angle 0.60822 / 0.34 (14067) hydrogen bonds : bond 0.04938 / 3.29 ( 474) hydrogen bonds : angle 6.23262 / 4.24 ( 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 122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.377 Fit side-chains REVERT: B 47 LEU cc_start: 0.7986 (tp) cc_final: 0.7574 (mt) REVERT: A 139 MET cc_start: 0.8488 (ppp) cc_final: 0.8147 (ptm) REVERT: C 11 ILE cc_start: 0.7794 (mt) cc_final: 0.7527 (mt) REVERT: D 37 MET cc_start: 0.7805 (ttp) cc_final: 0.7484 (ttt) REVERT: D 65 MET cc_start: 0.6955 (mmp) cc_final: 0.6678 (mmp) REVERT: D 269 PRO cc_start: 0.8600 (Cg_endo) cc_final: 0.8393 (Cg_exo) outliers start: 8 outliers final: 8 residues processed: 118 average time/residue: 0.0711 time to fit residues: 13.0413 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 : 0.217 ------------------------------------------------------------------------------- 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 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: 0.0670 chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.140424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109605 restraints weight = 16469.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.109724 restraints weight = 14088.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110376 restraints weight = 14826.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.111029 restraints weight = 11308.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.111387 restraints weight = 9765.666| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10221 Z= 0.132 Angle : 0.572 6.563 14067 Z= 0.319 Chirality : 0.044 0.171 1619 Planarity : 0.004 0.060 1589 Dihedral : 20.766 149.019 1939 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.25 % Allowed : 14.33 % Favored : 84.42 % 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: -1.50 (0.24), residues: 1103 helix: 0.46 (0.28), residues: 333 sheet: -1.22 (0.30), residues: 282 loop : -1.86 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 53 TYR 0.007 0.001 TYR B 211 PHE 0.010 0.001 PHE D 68 TRP 0.009 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (10221) covalent geometry : angle 0.57192 / 0.32 (14067) hydrogen bonds : bond 0.04340 / 2.88 ( 474) hydrogen bonds : angle 5.94652 / 4.04 ( 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 124 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.427 Fit side-chains REVERT: B 47 LEU cc_start: 0.7859 (tp) cc_final: 0.7583 (mt) REVERT: A 131 GLN cc_start: 0.7975 (pm20) cc_final: 0.7534 (pm20) REVERT: A 139 MET cc_start: 0.8457 (ppp) cc_final: 0.8025 (ptm) REVERT: C 11 ILE cc_start: 0.7838 (mt) cc_final: 0.7585 (mt) outliers start: 12 outliers final: 6 residues processed: 120 average time/residue: 0.0777 time to fit residues: 14.1661 Evaluate side-chains 111 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 135 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 102 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 77 optimal weight: 0.0370 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 ASN ** 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 = 0.3992 r_free = 0.3992 target = 0.140055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108924 restraints weight = 16388.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109899 restraints weight = 14086.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110937 restraints weight = 11917.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.111222 restraints weight = 9906.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111673 restraints weight = 8805.559| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10221 Z= 0.139 Angle : 0.580 7.967 14067 Z= 0.320 Chirality : 0.044 0.175 1619 Planarity : 0.004 0.061 1589 Dihedral : 20.741 148.018 1939 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.25 % Allowed : 16.10 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.24), residues: 1103 helix: 0.73 (0.29), residues: 334 sheet: -1.17 (0.30), residues: 282 loop : -1.78 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 261 TYR 0.006 0.001 TYR C 211 PHE 0.015 0.001 PHE D 68 TRP 0.006 0.001 TRP D 274 HIS 0.003 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (10221) covalent geometry : angle 0.58012 / 0.32 (14067) hydrogen bonds : bond 0.04187 / 2.77 ( 474) hydrogen bonds : angle 5.75753 / 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 127 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.323 Fit side-chains REVERT: A 131 GLN cc_start: 0.8035 (pm20) cc_final: 0.7525 (pm20) REVERT: A 139 MET cc_start: 0.8467 (ppp) cc_final: 0.8065 (ptm) REVERT: C 11 ILE cc_start: 0.7864 (mt) cc_final: 0.7632 (mt) REVERT: C 205 LEU cc_start: 0.8816 (mp) cc_final: 0.8545 (mt) REVERT: D 141 CYS cc_start: 0.7506 (m) cc_final: 0.7013 (m) outliers start: 12 outliers final: 8 residues processed: 122 average time/residue: 0.0713 time to fit residues: 13.5452 Evaluate side-chains 116 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 275 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 23 optimal weight: 0.1980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.138549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107130 restraints weight = 16578.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107348 restraints weight = 15700.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108530 restraints weight = 13396.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108918 restraints weight = 10667.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109243 restraints weight = 10366.737| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10221 Z= 0.168 Angle : 0.611 13.305 14067 Z= 0.328 Chirality : 0.045 0.173 1619 Planarity : 0.004 0.072 1589 Dihedral : 20.737 147.486 1939 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % 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: -1.19 (0.24), residues: 1103 helix: 0.87 (0.29), residues: 334 sheet: -1.15 (0.30), residues: 275 loop : -1.73 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 61 TYR 0.008 0.001 TYR C 239 PHE 0.017 0.001 PHE D 68 TRP 0.008 0.001 TRP D 274 HIS 0.005 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (10221) covalent geometry : angle 0.61132 / 0.33 (14067) hydrogen bonds : bond 0.04166 / 2.75 ( 474) hydrogen bonds : angle 5.66550 / 3.86 ( 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 127 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.374 Fit side-chains REVERT: B 47 LEU cc_start: 0.8112 (tp) cc_final: 0.7570 (mt) REVERT: A 131 GLN cc_start: 0.8099 (pm20) cc_final: 0.7613 (pm20) REVERT: A 139 MET cc_start: 0.8459 (ppp) cc_final: 0.8085 (ptm) REVERT: C 11 ILE cc_start: 0.7896 (mt) cc_final: 0.7636 (mt) REVERT: C 25 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7221 (mm-30) REVERT: C 205 LEU cc_start: 0.8918 (mp) cc_final: 0.8623 (mt) REVERT: D 180 MET cc_start: 0.8592 (mmm) cc_final: 0.8170 (mpp) REVERT: D 304 GLU cc_start: 0.6804 (pm20) cc_final: 0.6107 (tp30) outliers start: 18 outliers final: 13 residues processed: 121 average time/residue: 0.0682 time to fit residues: 13.1578 Evaluate side-chains 115 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain D residue 296 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 131 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 = 0.3972 r_free = 0.3972 target = 0.138724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107700 restraints weight = 16376.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107695 restraints weight = 14719.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109178 restraints weight = 13575.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109448 restraints weight = 10683.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109666 restraints weight = 10208.486| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10221 Z= 0.148 Angle : 0.598 7.413 14067 Z= 0.326 Chirality : 0.045 0.276 1619 Planarity : 0.004 0.077 1589 Dihedral : 20.729 147.267 1939 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.97 % Allowed : 17.45 % Favored : 80.58 % 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: -1.17 (0.24), residues: 1103 helix: 0.93 (0.29), residues: 333 sheet: -1.24 (0.29), residues: 283 loop : -1.67 (0.25), residues: 487 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 0.012 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 0.00319 / 0.15 (10221) covalent geometry : angle 0.59779 / 0.33 (14067) hydrogen bonds : bond 0.04062 / 2.65 ( 474) hydrogen bonds : angle 5.62269 / 3.83 ( 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 129 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.318 Fit side-chains REVERT: A 131 GLN cc_start: 0.8103 (pm20) cc_final: 0.7608 (pm20) REVERT: A 139 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8030 (ptm) REVERT: C 11 ILE cc_start: 0.7890 (mt) cc_final: 0.7634 (mt) REVERT: C 25 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7206 (mm-30) REVERT: D 160 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5849 (mt-10) REVERT: D 304 GLU cc_start: 0.6811 (pm20) cc_final: 0.6199 (tp30) outliers start: 19 outliers final: 11 residues processed: 123 average time/residue: 0.0692 time to fit residues: 13.3156 Evaluate side-chains 114 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 296 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 110 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 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 = 0.3973 r_free = 0.3973 target = 0.138772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107281 restraints weight = 16208.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107672 restraints weight = 15421.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.109242 restraints weight = 13579.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.109556 restraints weight = 10933.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110011 restraints weight = 10230.531| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10221 Z= 0.148 Angle : 0.606 9.548 14067 Z= 0.327 Chirality : 0.045 0.250 1619 Planarity : 0.004 0.076 1589 Dihedral : 20.723 147.115 1939 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.56 % Allowed : 17.76 % Favored : 80.69 % 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: 1.00 (0.29), residues: 333 sheet: -1.34 (0.29), residues: 288 loop : -1.62 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 149 TYR 0.011 0.001 TYR C 239 PHE 0.016 0.001 PHE D 309 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 0.00320 / 0.15 (10221) covalent geometry : angle 0.60617 / 0.33 (14067) hydrogen bonds : bond 0.03990 / 2.58 ( 474) hydrogen bonds : angle 5.55950 / 3.79 ( 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 125 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.414 Fit side-chains REVERT: A 131 GLN cc_start: 0.8114 (pm20) cc_final: 0.7654 (pm20) REVERT: A 139 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8043 (ptm) REVERT: C 11 ILE cc_start: 0.7911 (mt) cc_final: 0.7662 (mt) REVERT: C 25 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7233 (mm-30) REVERT: C 68 MET cc_start: 0.8446 (pmm) cc_final: 0.8145 (pmm) REVERT: D 160 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5872 (mt-10) REVERT: D 304 GLU cc_start: 0.6698 (pm20) cc_final: 0.6191 (tp30) outliers start: 15 outliers final: 11 residues processed: 120 average time/residue: 0.0708 time to fit residues: 13.4583 Evaluate side-chains 117 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 296 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.135787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103884 restraints weight = 16348.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104271 restraints weight = 14154.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.104907 restraints weight = 14417.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105492 restraints weight = 11381.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105704 restraints weight = 10392.407| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10221 Z= 0.221 Angle : 0.659 9.927 14067 Z= 0.355 Chirality : 0.047 0.276 1619 Planarity : 0.004 0.079 1589 Dihedral : 20.822 146.541 1939 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.66 % Allowed : 17.86 % Favored : 80.48 % 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: -1.29 (0.24), residues: 1103 helix: 0.94 (0.29), residues: 331 sheet: -1.47 (0.28), residues: 300 loop : -1.70 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 149 TYR 0.022 0.002 TYR B 250 PHE 0.013 0.002 PHE A 144 TRP 0.006 0.001 TRP D 274 HIS 0.009 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (10221) covalent geometry : angle 0.65858 / 0.36 (14067) hydrogen bonds : bond 0.04296 / 2.76 ( 474) hydrogen bonds : angle 5.72474 / 3.88 ( 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 123 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.226 Fit side-chains REVERT: A 108 GLN cc_start: 0.8135 (mp10) cc_final: 0.7842 (mp10) REVERT: A 131 GLN cc_start: 0.8301 (pm20) cc_final: 0.7834 (pm20) REVERT: A 139 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8106 (ptm) REVERT: C 25 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7313 (mm-30) REVERT: C 38 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7800 (tm-30) REVERT: D 160 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6033 (mt-10) REVERT: D 304 GLU cc_start: 0.6758 (pm20) cc_final: 0.6209 (tp30) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 0.0701 time to fit residues: 12.6356 Evaluate side-chains 114 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 58 ASP 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 Chi-restraints excluded: chain D residue 296 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 18 optimal weight: 0.0170 chunk 103 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 98 optimal weight: 0.1980 overall best weight: 0.3418 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.138792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107249 restraints weight = 16126.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107869 restraints weight = 13618.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108568 restraints weight = 13469.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109294 restraints weight = 11199.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.110649 restraints weight = 10164.826| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10221 Z= 0.136 Angle : 0.620 7.775 14067 Z= 0.335 Chirality : 0.045 0.243 1619 Planarity : 0.004 0.076 1589 Dihedral : 20.728 146.568 1939 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.45 % Allowed : 18.28 % Favored : 80.27 % 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: 0.99 (0.29), residues: 333 sheet: -1.41 (0.29), residues: 281 loop : -1.56 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 146 TYR 0.009 0.002 TYR A 249 PHE 0.020 0.001 PHE D 309 TRP 0.010 0.001 TRP A 28 HIS 0.012 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (10221) covalent geometry : angle 0.61969 / 0.34 (14067) hydrogen bonds : bond 0.03970 / 2.51 ( 474) hydrogen bonds : angle 5.62718 / 3.83 ( 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 120 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.375 Fit side-chains REVERT: A 108 GLN cc_start: 0.8137 (mp10) cc_final: 0.7848 (mp10) REVERT: A 131 GLN cc_start: 0.8224 (pm20) cc_final: 0.7770 (pm20) REVERT: A 139 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8046 (ptm) REVERT: C 25 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7240 (mm-30) REVERT: D 160 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5802 (mt-10) REVERT: D 180 MET cc_start: 0.8526 (mmm) cc_final: 0.8098 (mpp) REVERT: D 304 GLU cc_start: 0.6696 (pm20) cc_final: 0.6166 (tp30) outliers start: 14 outliers final: 12 residues processed: 116 average time/residue: 0.0684 time to fit residues: 12.3627 Evaluate side-chains 114 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 39 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 48 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.138657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.106667 restraints weight = 16376.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107454 restraints weight = 14427.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108126 restraints weight = 13334.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108800 restraints weight = 11190.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109426 restraints weight = 10309.857| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10221 Z= 0.145 Angle : 0.625 12.122 14067 Z= 0.335 Chirality : 0.045 0.275 1619 Planarity : 0.004 0.071 1589 Dihedral : 20.716 146.817 1939 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.77 % Allowed : 18.59 % Favored : 79.65 % 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: -1.13 (0.24), residues: 1103 helix: 1.02 (0.29), residues: 333 sheet: -1.39 (0.28), residues: 286 loop : -1.55 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 149 TYR 0.010 0.002 TYR C 239 PHE 0.014 0.001 PHE D 68 TRP 0.008 0.001 TRP D 274 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (10221) covalent geometry : angle 0.62463 / 0.33 (14067) hydrogen bonds : bond 0.04007 / 2.51 ( 474) hydrogen bonds : angle 5.57241 / 3.79 ( 1306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1455.99 seconds wall clock time: 26 minutes 4.44 seconds (1564.44 seconds total)