Starting phenix.real_space_refine on Wed Sep 17 17:45:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yju_39350/09_2025/8yju_39350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yju_39350/09_2025/8yju_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_39350/09_2025/8yju_39350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yju_39350/09_2025/8yju_39350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yju_39350/09_2025/8yju_39350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yju_39350/09_2025/8yju_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-2.0-5805/lib/python3.9/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: 2.43, per 1000 atoms: 0.24 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: 0.78 Conformation dependent library (CDL) restraints added in 317.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.99 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: 1.93 Time building geometry restraints manager: 1.00 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=" CG1 ILE D 72 " pdb=" CD1 ILE D 72 " ideal model delta sigma weight residual 1.513 1.426 0.087 3.90e-02 6.57e+02 4.99e+00 bond pdb=" C VAL A 233 " pdb=" N PRO A 234 " ideal model delta sigma weight residual 1.331 1.358 -0.026 1.20e-02 6.94e+03 4.86e+00 bond pdb=" CA ILE D 72 " pdb=" CB ILE D 72 " ideal model delta sigma weight residual 1.540 1.565 -0.024 1.25e-02 6.40e+03 3.82e+00 bond pdb=" CB ASP D 34 " pdb=" CG ASP D 34 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.20e+00 bond pdb=" CG ARG B 149 " pdb=" CD ARG B 149 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.09e+00 ... (remaining 10216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 13668 2.64 - 5.28: 310 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: 1292 0.063 - 0.125: 269 0.125 - 0.188: 48 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: 0.010 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.820 Find NCS groups from input model: 0.120 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.005 0.087 10221 Z= 0.238 Angle : 1.025 13.187 14067 Z= 0.527 Chirality : 0.056 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 aren 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 covalent geometry : bond 0.00529 (10221) covalent geometry : angle 1.02509 (14067) hydrogen bonds : bond 0.21497 ( 474) hydrogen bonds : angle 9.51251 ( 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 : 0.336 Fit side-chains revert: symmetry clash REVERT: B 150 ASP cc_start: 0.7795 (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: 0.8189 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0783 time to fit residues: 17.3471 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 : 0.281 ------------------------------------------------------------------------------- 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: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: B 49 GLN A 204 GLN C 24 ASN C 200 ASN ** 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 = 0.3969 r_free = 0.3969 target = 0.138234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107061 restraints weight = 16355.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107202 restraints weight = 14933.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107943 restraints weight = 13718.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108577 restraints weight = 11422.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.109133 restraints weight = 10603.221| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10221 Z= 0.223 Angle : 0.664 6.271 14067 Z= 0.365 Chirality : 0.045 0.155 1619 Planarity : 0.005 0.063 1589 Dihedral : 21.003 148.748 1939 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.62 % Allowed : 10.38 % Favored : 88.99 % 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 aren not related in a simple way. whole: -2.21 (0.22), residues: 1103 helix: -0.66 (0.26), residues: 324 sheet: -1.33 (0.29), residues: 289 loop : -2.04 (0.23), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 53 TYR 0.011 0.002 TYR B 239 PHE 0.016 0.002 PHE A 144 TRP 0.017 0.002 TRP D 274 HIS 0.004 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00499 (10221) covalent geometry : angle 0.66383 (14067) hydrogen bonds : bond 0.05125 ( 474) hydrogen bonds : angle 6.34657 ( 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 132 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.308 Fit side-chains REVERT: D 37 MET cc_start: 0.7872 (ttp) cc_final: 0.7588 (ttt) outliers start: 6 outliers final: 4 residues processed: 128 average time/residue: 0.0738 time to fit residues: 14.5233 Evaluate side-chains 106 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 HIS ** 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 = 0.3969 r_free = 0.3969 target = 0.138392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107337 restraints weight = 16363.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107626 restraints weight = 14169.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108289 restraints weight = 13811.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108898 restraints weight = 11315.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109246 restraints weight = 10475.193| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10221 Z= 0.164 Angle : 0.592 6.065 14067 Z= 0.325 Chirality : 0.043 0.151 1619 Planarity : 0.004 0.052 1589 Dihedral : 20.715 144.753 1939 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.25 % Allowed : 12.88 % Favored : 85.88 % 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 aren not related in a simple way. whole: -1.66 (0.24), residues: 1103 helix: 0.26 (0.28), residues: 332 sheet: -1.38 (0.29), residues: 289 loop : -1.83 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 53 TYR 0.007 0.001 TYR B 239 PHE 0.010 0.001 PHE D 42 TRP 0.011 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00367 (10221) covalent geometry : angle 0.59187 (14067) hydrogen bonds : bond 0.04291 ( 474) hydrogen bonds : angle 5.88543 ( 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 132 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.365 Fit side-chains REVERT: A 75 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7745 (tmm) REVERT: A 108 GLN cc_start: 0.8221 (mp10) cc_final: 0.7852 (mp10) REVERT: C 11 ILE cc_start: 0.7892 (mt) cc_final: 0.7676 (mt) REVERT: C 205 LEU cc_start: 0.8716 (mp) cc_final: 0.8451 (mt) REVERT: D 37 MET cc_start: 0.7848 (ttp) cc_final: 0.7617 (ttt) outliers start: 12 outliers final: 9 residues processed: 125 average time/residue: 0.0732 time to fit residues: 14.2755 Evaluate side-chains 113 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 75 MET 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 131 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 296 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 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 = 0.3971 r_free = 0.3971 target = 0.138770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107102 restraints weight = 16404.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107682 restraints weight = 14289.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108454 restraints weight = 13149.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.109564 restraints weight = 11150.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110160 restraints weight = 10422.515| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2744 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= 0.145 Angle : 0.568 6.255 14067 Z= 0.313 Chirality : 0.043 0.222 1619 Planarity : 0.004 0.066 1589 Dihedral : 20.697 145.227 1939 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.56 % Allowed : 16.30 % Favored : 82.14 % 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 aren not related in a simple way. whole: -1.25 (0.24), residues: 1103 helix: 0.79 (0.28), residues: 334 sheet: -1.22 (0.29), residues: 280 loop : -1.71 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.008 0.001 TYR D 40 PHE 0.014 0.001 PHE D 42 TRP 0.010 0.001 TRP D 274 HIS 0.005 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00325 (10221) covalent geometry : angle 0.56807 (14067) hydrogen bonds : bond 0.03909 ( 474) hydrogen bonds : angle 5.60482 ( 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 126 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7545 (tmm) REVERT: C 11 ILE cc_start: 0.7937 (mt) cc_final: 0.7675 (mt) REVERT: C 205 LEU cc_start: 0.8802 (mp) cc_final: 0.8587 (mt) REVERT: D 37 MET cc_start: 0.7803 (ttp) cc_final: 0.7557 (ttt) outliers start: 15 outliers final: 8 residues processed: 120 average time/residue: 0.0741 time to fit residues: 13.7736 Evaluate side-chains 108 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain A residue 75 MET 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 131 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 296 LEU 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: 0.6980 chunk 102 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4096 r_free = 0.4096 target = 0.146201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.116791 restraints weight = 16290.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.116407 restraints weight = 16883.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.117483 restraints weight = 16734.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.117799 restraints weight = 12522.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.118424 restraints weight = 12019.037| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10221 Z= 0.163 Angle : 0.581 6.749 14067 Z= 0.318 Chirality : 0.043 0.242 1619 Planarity : 0.004 0.068 1589 Dihedral : 20.639 144.897 1939 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.87 % Allowed : 16.82 % Favored : 81.31 % 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 aren not related in a simple way. whole: -1.20 (0.24), residues: 1103 helix: 0.92 (0.29), residues: 333 sheet: -1.36 (0.28), residues: 290 loop : -1.62 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 61 TYR 0.009 0.002 TYR C 114 PHE 0.019 0.001 PHE D 68 TRP 0.009 0.001 TRP B 28 HIS 0.005 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00371 (10221) covalent geometry : angle 0.58106 (14067) hydrogen bonds : bond 0.03953 ( 474) hydrogen bonds : angle 5.58456 ( 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 128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8168 (tt) REVERT: A 75 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7654 (tmm) REVERT: A 156 ASP cc_start: 0.7037 (t70) cc_final: 0.6836 (t70) REVERT: C 11 ILE cc_start: 0.7853 (mt) cc_final: 0.7589 (mt) REVERT: C 205 LEU cc_start: 0.8646 (mp) cc_final: 0.8313 (mt) outliers start: 18 outliers final: 10 residues processed: 123 average time/residue: 0.0762 time to fit residues: 14.3833 Evaluate side-chains 112 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 37 LEU Chi-restraints excluded: chain A residue 75 MET 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 131 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 296 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 114 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.146756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117336 restraints weight = 16582.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.116770 restraints weight = 17917.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.118208 restraints weight = 16452.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118414 restraints weight = 12506.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.119082 restraints weight = 11869.364| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3180 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= 0.149 Angle : 0.575 6.464 14067 Z= 0.314 Chirality : 0.043 0.218 1619 Planarity : 0.004 0.065 1589 Dihedral : 20.632 144.866 1939 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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 aren not related in a simple way. whole: -1.10 (0.24), residues: 1103 helix: 1.06 (0.29), residues: 333 sheet: -1.35 (0.28), residues: 288 loop : -1.58 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 149 TYR 0.011 0.001 TYR C 239 PHE 0.020 0.001 PHE D 68 TRP 0.014 0.001 TRP B 28 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00340 (10221) covalent geometry : angle 0.57466 (14067) hydrogen bonds : bond 0.03875 ( 474) hydrogen bonds : angle 5.51210 ( 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 130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: B 90 LEU cc_start: 0.8973 (mm) cc_final: 0.8662 (mp) REVERT: A 25 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6718 (mt-10) REVERT: A 75 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7501 (tmm) REVERT: A 156 ASP cc_start: 0.7041 (t70) cc_final: 0.6762 (t70) REVERT: C 11 ILE cc_start: 0.7896 (mt) cc_final: 0.7602 (mt) REVERT: D 40 TYR cc_start: 0.7745 (m-10) cc_final: 0.7358 (m-10) REVERT: D 160 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.6005 (mt-10) outliers start: 20 outliers final: 13 residues processed: 124 average time/residue: 0.0814 time to fit residues: 15.3768 Evaluate side-chains 115 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 75 MET 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 15 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 131 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3936 r_free = 0.3936 target = 0.136307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103929 restraints weight = 16474.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105153 restraints weight = 14398.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105438 restraints weight = 13140.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106260 restraints weight = 11319.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106322 restraints weight = 10190.642| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10221 Z= 0.181 Angle : 0.610 8.001 14067 Z= 0.329 Chirality : 0.044 0.221 1619 Planarity : 0.004 0.060 1589 Dihedral : 20.705 144.422 1939 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.18 % Allowed : 18.17 % 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 aren not related in a simple way. whole: -1.09 (0.25), residues: 1103 helix: 1.08 (0.29), residues: 334 sheet: -1.45 (0.28), residues: 281 loop : -1.51 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 149 TYR 0.012 0.002 TYR C 239 PHE 0.020 0.002 PHE D 68 TRP 0.008 0.001 TRP B 28 HIS 0.005 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00418 (10221) covalent geometry : angle 0.60962 (14067) hydrogen bonds : bond 0.03937 ( 474) hydrogen bonds : angle 5.54659 ( 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: 21 poor density : 108 time to evaluate : 0.345 Fit side-chains REVERT: A 68 MET cc_start: 0.8432 (pmm) cc_final: 0.8199 (pmm) REVERT: A 75 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7521 (tmm) REVERT: C 11 ILE cc_start: 0.7935 (mt) cc_final: 0.7723 (mt) REVERT: D 37 MET cc_start: 0.7900 (ttp) cc_final: 0.7635 (ttt) REVERT: D 160 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6094 (mt-10) outliers start: 21 outliers final: 17 residues processed: 121 average time/residue: 0.0718 time to fit residues: 13.7358 Evaluate side-chains 120 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 75 MET 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 15 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 65 ASN 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 131 VAL Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 177 THR 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: 0.1980 chunk 86 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.142399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.112519 restraints weight = 16265.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112151 restraints weight = 18237.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.112985 restraints weight = 19029.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113669 restraints weight = 13994.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115190 restraints weight = 12086.114| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10221 Z= 0.241 Angle : 0.665 10.809 14067 Z= 0.356 Chirality : 0.045 0.206 1619 Planarity : 0.004 0.059 1589 Dihedral : 20.824 143.305 1939 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.60 % Allowed : 18.69 % Favored : 78.71 % 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 aren not related in a simple way. whole: -1.30 (0.24), residues: 1103 helix: 0.93 (0.28), residues: 334 sheet: -1.59 (0.27), residues: 300 loop : -1.61 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 70 TYR 0.013 0.002 TYR C 239 PHE 0.015 0.002 PHE D 68 TRP 0.013 0.002 TRP B 28 HIS 0.005 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00559 (10221) covalent geometry : angle 0.66518 (14067) hydrogen bonds : bond 0.04269 ( 474) hydrogen bonds : angle 5.75755 ( 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 127 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.364 Fit side-chains REVERT: A 75 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7505 (tmm) REVERT: C 68 MET cc_start: 0.8740 (pmm) cc_final: 0.8429 (pmm) REVERT: D 37 MET cc_start: 0.7958 (ttp) cc_final: 0.7680 (ttt) REVERT: D 160 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6267 (mt-10) REVERT: D 180 MET cc_start: 0.8358 (mmm) cc_final: 0.7749 (mmm) outliers start: 25 outliers final: 20 residues processed: 118 average time/residue: 0.0718 time to fit residues: 13.3101 Evaluate side-chains 123 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain A residue 75 MET 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 15 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 65 ASN 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 131 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 189 VAL 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: 0.6980 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4049 r_free = 0.4049 target = 0.142381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112268 restraints weight = 16318.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112058 restraints weight = 17153.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.113342 restraints weight = 17155.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113520 restraints weight = 12620.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.113623 restraints weight = 14091.851| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10221 Z= 0.231 Angle : 0.666 10.338 14067 Z= 0.355 Chirality : 0.045 0.208 1619 Planarity : 0.004 0.062 1589 Dihedral : 20.836 143.272 1939 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.18 % Allowed : 19.73 % Favored : 78.09 % 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 aren not related in a simple way. whole: -1.36 (0.24), residues: 1103 helix: 0.88 (0.28), residues: 334 sheet: -1.74 (0.28), residues: 280 loop : -1.59 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.011 0.002 TYR C 239 PHE 0.018 0.002 PHE D 68 TRP 0.010 0.002 TRP B 28 HIS 0.006 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00537 (10221) covalent geometry : angle 0.66630 (14067) hydrogen bonds : bond 0.04216 ( 474) hydrogen bonds : angle 5.74656 ( 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: 21 poor density : 102 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7494 (tmm) REVERT: A 108 GLN cc_start: 0.8016 (mp10) cc_final: 0.7754 (mp10) REVERT: C 68 MET cc_start: 0.8722 (pmm) cc_final: 0.8327 (pmm) REVERT: D 160 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6338 (mt-10) REVERT: D 180 MET cc_start: 0.8295 (mmm) cc_final: 0.7773 (mmm) outliers start: 21 outliers final: 18 residues processed: 115 average time/residue: 0.0778 time to fit residues: 14.0488 Evaluate side-chains 119 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 75 MET 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 11 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 ASN 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 131 VAL Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 189 VAL 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: 3.9990 chunk 30 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 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 = 0.4070 r_free = 0.4070 target = 0.144083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.114107 restraints weight = 16227.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113900 restraints weight = 17704.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.115203 restraints weight = 19362.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.115389 restraints weight = 13186.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115670 restraints weight = 13726.070| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10221 Z= 0.172 Angle : 0.627 9.868 14067 Z= 0.337 Chirality : 0.044 0.205 1619 Planarity : 0.004 0.061 1589 Dihedral : 20.807 143.574 1939 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.28 % Allowed : 19.63 % Favored : 78.09 % 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 aren not related in a simple way. whole: -1.24 (0.24), residues: 1103 helix: 1.02 (0.28), residues: 334 sheet: -1.69 (0.28), residues: 280 loop : -1.54 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 149 TYR 0.010 0.002 TYR D 40 PHE 0.020 0.001 PHE D 68 TRP 0.010 0.002 TRP B 28 HIS 0.005 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00397 (10221) covalent geometry : angle 0.62732 (14067) hydrogen bonds : bond 0.03997 ( 474) hydrogen bonds : angle 5.63097 ( 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 126 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7482 (tmm) REVERT: A 108 GLN cc_start: 0.8008 (mp10) cc_final: 0.7775 (mp10) REVERT: A 131 GLN cc_start: 0.7422 (pm20) cc_final: 0.6885 (pm20) REVERT: C 68 MET cc_start: 0.8685 (pmm) cc_final: 0.8249 (pmm) REVERT: D 160 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6235 (mt-10) REVERT: D 180 MET cc_start: 0.8276 (mmm) cc_final: 0.7736 (mmm) outliers start: 22 outliers final: 17 residues processed: 119 average time/residue: 0.0716 time to fit residues: 13.3703 Evaluate side-chains 119 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 75 MET 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 11 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 ASN 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 177 THR Chi-restraints excluded: chain D residue 189 VAL 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 74 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 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 = 0.4069 r_free = 0.4069 target = 0.144038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113998 restraints weight = 16473.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.113799 restraints weight = 17330.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115009 restraints weight = 17271.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115125 restraints weight = 13209.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.116071 restraints weight = 12190.630| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10221 Z= 0.176 Angle : 0.631 10.679 14067 Z= 0.338 Chirality : 0.044 0.204 1619 Planarity : 0.004 0.061 1589 Dihedral : 20.799 143.666 1939 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.18 % Allowed : 20.04 % Favored : 77.78 % 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 aren not related in a simple way. whole: -1.24 (0.24), residues: 1103 helix: 1.06 (0.28), residues: 334 sheet: -1.66 (0.28), residues: 286 loop : -1.58 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 149 TYR 0.011 0.002 TYR D 40 PHE 0.020 0.001 PHE D 68 TRP 0.009 0.002 TRP B 28 HIS 0.005 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00412 (10221) covalent geometry : angle 0.63140 (14067) hydrogen bonds : bond 0.04023 ( 474) hydrogen bonds : angle 5.60377 ( 1306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1487.02 seconds wall clock time: 26 minutes 38.36 seconds (1598.36 seconds total)