Starting phenix.real_space_refine on Mon Jun 9 02:10:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yju_39350/06_2025/8yju_39350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yju_39350/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yju_39350/06_2025/8yju_39350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yju_39350/06_2025/8yju_39350.map" model { file = "/net/cci-nas-00/data/ceres_data/8yju_39350/06_2025/8yju_39350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yju_39350/06_2025/8yju_39350.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.30, per 1000 atoms: 0.63 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: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.35 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: 3.35 Time building geometry restraints manager: 2.96 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: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.140 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.002 TRP D 274 HIS 0.008 0.002 HIS D 63 PHE 0.024 0.003 PHE D 42 TYR 0.030 0.003 TYR B 249 ARG 0.015 0.001 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.21497 ( 474) hydrogen bonds : angle 9.51251 ( 1306) covalent geometry : bond 0.00529 (10221) covalent geometry : angle 1.02509 (14067) *********************** 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 : 1.040 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: 0.1754 time to fit residues: 38.2106 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 : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.139420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108126 restraints weight = 16256.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108574 restraints weight = 14502.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.109632 restraints weight = 13695.083| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1769 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= 0.203 Angle : 0.647 6.095 14067 Z= 0.356 Chirality : 0.045 0.156 1619 Planarity : 0.005 0.063 1589 Dihedral : 20.931 148.987 1939 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.73 % Allowed : 9.87 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.22), residues: 1103 helix: -0.71 (0.26), residues: 324 sheet: -1.27 (0.30), residues: 288 loop : -2.06 (0.23), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 274 HIS 0.003 0.001 HIS D 253 PHE 0.013 0.002 PHE A 144 TYR 0.012 0.002 TYR B 239 ARG 0.006 0.001 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 474) hydrogen bonds : angle 6.40110 ( 1306) covalent geometry : bond 0.00451 (10221) covalent geometry : angle 0.64665 (14067) *********************** 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 135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.020 Fit side-chains REVERT: D 37 MET cc_start: 0.7858 (ttp) cc_final: 0.7584 (ttt) REVERT: D 269 PRO cc_start: 0.8583 (Cg_endo) cc_final: 0.8375 (Cg_exo) outliers start: 7 outliers final: 4 residues processed: 130 average time/residue: 0.1861 time to fit residues: 37.1363 Evaluate side-chains 108 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 53 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 98 optimal weight: 0.0010 chunk 71 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3992 r_free = 0.3992 target = 0.140057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.108993 restraints weight = 16427.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109106 restraints weight = 15436.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.110366 restraints weight = 13251.234| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10221 Z= 0.145 Angle : 0.581 6.012 14067 Z= 0.319 Chirality : 0.043 0.150 1619 Planarity : 0.004 0.052 1589 Dihedral : 20.664 145.215 1939 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.04 % Allowed : 12.56 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.24), residues: 1103 helix: 0.30 (0.28), residues: 331 sheet: -1.28 (0.29), residues: 288 loop : -1.83 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 274 HIS 0.003 0.001 HIS D 63 PHE 0.009 0.001 PHE D 42 TYR 0.008 0.001 TYR B 239 ARG 0.003 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 474) hydrogen bonds : angle 5.85166 ( 1306) covalent geometry : bond 0.00324 (10221) covalent geometry : angle 0.58060 (14067) *********************** 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 130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.085 Fit side-chains REVERT: A 75 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7756 (tmm) REVERT: C 11 ILE cc_start: 0.7826 (mt) cc_final: 0.7602 (mt) REVERT: D 37 MET cc_start: 0.7760 (ttp) cc_final: 0.7537 (ttt) REVERT: D 65 MET cc_start: 0.6949 (mmp) cc_final: 0.6679 (mmp) outliers start: 10 outliers final: 7 residues processed: 122 average time/residue: 0.1793 time to fit residues: 34.0716 Evaluate side-chains 114 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** 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 = 0.3971 r_free = 0.3971 target = 0.138572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107026 restraints weight = 16235.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.107530 restraints weight = 13829.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108164 restraints weight = 13454.069| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10221 Z= 0.153 Angle : 0.574 6.303 14067 Z= 0.315 Chirality : 0.043 0.210 1619 Planarity : 0.004 0.066 1589 Dihedral : 20.687 145.158 1939 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.77 % Allowed : 15.47 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.24), residues: 1103 helix: 0.76 (0.28), residues: 334 sheet: -1.16 (0.29), residues: 285 loop : -1.69 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.005 0.001 HIS D 63 PHE 0.013 0.001 PHE D 42 TYR 0.008 0.001 TYR C 239 ARG 0.002 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 474) hydrogen bonds : angle 5.60135 ( 1306) covalent geometry : bond 0.00343 (10221) covalent geometry : angle 0.57410 (14067) *********************** 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 129 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 2.049 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7541 (tmm) REVERT: C 11 ILE cc_start: 0.7941 (mt) cc_final: 0.7673 (mt) REVERT: D 37 MET cc_start: 0.7747 (ttp) cc_final: 0.7546 (ttt) outliers start: 17 outliers final: 9 residues processed: 122 average time/residue: 0.2685 time to fit residues: 53.9130 Evaluate side-chains 109 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 2.844 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.138437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106645 restraints weight = 16153.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107349 restraints weight = 14524.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108059 restraints weight = 13313.782| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10221 Z= 0.150 Angle : 0.574 6.598 14067 Z= 0.313 Chirality : 0.043 0.244 1619 Planarity : 0.004 0.069 1589 Dihedral : 20.605 145.232 1939 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.56 % Allowed : 17.03 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1103 helix: 0.92 (0.29), residues: 333 sheet: -1.26 (0.29), residues: 285 loop : -1.65 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.005 0.001 HIS D 63 PHE 0.018 0.001 PHE D 68 TYR 0.011 0.001 TYR C 239 ARG 0.002 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 474) hydrogen bonds : angle 5.52546 ( 1306) covalent geometry : bond 0.00339 (10221) covalent geometry : angle 0.57425 (14067) *********************** 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 125 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8333 (tt) REVERT: A 75 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7531 (tmm) REVERT: A 131 GLN cc_start: 0.8172 (pm20) cc_final: 0.7748 (pm20) REVERT: C 11 ILE cc_start: 0.7853 (mt) cc_final: 0.7580 (mt) REVERT: C 205 LEU cc_start: 0.8807 (mp) cc_final: 0.8554 (mt) outliers start: 15 outliers final: 10 residues processed: 121 average time/residue: 0.2583 time to fit residues: 47.9185 Evaluate side-chains 114 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 0.0060 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.138605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.106656 restraints weight = 16305.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107282 restraints weight = 14477.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.108014 restraints weight = 13346.318| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3075 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= 0.150 Angle : 0.573 6.374 14067 Z= 0.314 Chirality : 0.043 0.217 1619 Planarity : 0.004 0.067 1589 Dihedral : 20.584 145.113 1939 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.77 % Allowed : 17.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.24), residues: 1103 helix: 1.05 (0.29), residues: 333 sheet: -1.24 (0.29), residues: 290 loop : -1.61 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 PHE 0.019 0.001 PHE D 68 TYR 0.010 0.001 TYR C 114 ARG 0.005 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 474) hydrogen bonds : angle 5.45645 ( 1306) covalent geometry : bond 0.00341 (10221) covalent geometry : angle 0.57327 (14067) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.373 Fit side-chains REVERT: B 37 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8354 (tt) REVERT: B 90 LEU cc_start: 0.8917 (mm) cc_final: 0.8656 (mp) REVERT: A 75 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7412 (tmm) REVERT: A 131 GLN cc_start: 0.8205 (pm20) cc_final: 0.7743 (pm20) REVERT: C 11 ILE cc_start: 0.7902 (mt) cc_final: 0.7591 (mt) REVERT: C 25 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7236 (mm-30) REVERT: D 160 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5829 (mt-10) REVERT: D 180 MET cc_start: 0.8523 (mmm) cc_final: 0.8114 (mpp) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 0.2315 time to fit residues: 44.2721 Evaluate side-chains 113 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.0010 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.144230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.114599 restraints weight = 16467.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.113805 restraints weight = 17172.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.115109 restraints weight = 16994.521| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10221 Z= 0.217 Angle : 0.632 6.663 14067 Z= 0.342 Chirality : 0.044 0.218 1619 Planarity : 0.004 0.065 1589 Dihedral : 20.747 144.026 1939 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.87 % Allowed : 18.28 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.24), residues: 1103 helix: 0.97 (0.28), residues: 334 sheet: -1.44 (0.28), residues: 283 loop : -1.58 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 28 HIS 0.004 0.001 HIS D 63 PHE 0.019 0.002 PHE D 68 TYR 0.012 0.002 TYR C 239 ARG 0.004 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 474) hydrogen bonds : angle 5.64357 ( 1306) covalent geometry : bond 0.00501 (10221) covalent geometry : angle 0.63244 (14067) *********************** 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 124 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.002 Fit side-chains REVERT: A 25 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6748 (mt-10) REVERT: A 75 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7364 (tmm) REVERT: A 131 GLN cc_start: 0.8139 (pm20) cc_final: 0.7647 (pm20) REVERT: C 205 LEU cc_start: 0.8901 (mp) cc_final: 0.8692 (mt) outliers start: 18 outliers final: 13 residues processed: 120 average time/residue: 0.1739 time to fit residues: 32.0954 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 : 1.041 ------------------------------------------------------------------------------- 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 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 102 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 64 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 chunk 55 optimal weight: 0.0470 chunk 82 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.146984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117407 restraints weight = 16376.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116755 restraints weight = 17195.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118221 restraints weight = 18555.618| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10221 Z= 0.144 Angle : 0.596 7.750 14067 Z= 0.323 Chirality : 0.043 0.213 1619 Planarity : 0.004 0.061 1589 Dihedral : 20.687 144.689 1939 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.56 % Allowed : 18.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1103 helix: 1.15 (0.29), residues: 334 sheet: -1.40 (0.29), residues: 285 loop : -1.52 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.004 0.001 HIS C 44 PHE 0.019 0.001 PHE D 68 TYR 0.010 0.001 TYR C 239 ARG 0.003 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 474) hydrogen bonds : angle 5.49962 ( 1306) covalent geometry : bond 0.00335 (10221) covalent geometry : angle 0.59566 (14067) *********************** 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 128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.982 Fit side-chains REVERT: B 1 MET cc_start: 0.7423 (ppp) cc_final: 0.6939 (ptt) REVERT: B 90 LEU cc_start: 0.8974 (mm) cc_final: 0.8664 (mp) REVERT: A 75 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7421 (tmm) REVERT: A 131 GLN cc_start: 0.8001 (pm20) cc_final: 0.7572 (pm20) REVERT: C 68 MET cc_start: 0.8474 (pmm) cc_final: 0.8076 (pmm) REVERT: D 65 MET cc_start: 0.6892 (mmp) cc_final: 0.6687 (mmp) REVERT: D 160 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5689 (mt-10) REVERT: D 180 MET cc_start: 0.8413 (mmm) cc_final: 0.8072 (mpp) outliers start: 15 outliers final: 11 residues processed: 123 average time/residue: 0.2057 time to fit residues: 39.1266 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 : 1.132 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain D residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 76 optimal weight: 0.0870 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.147182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.117541 restraints weight = 16411.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.117056 restraints weight = 16477.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.117699 restraints weight = 16970.547| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10221 Z= 0.142 Angle : 0.610 12.640 14067 Z= 0.327 Chirality : 0.043 0.211 1619 Planarity : 0.004 0.062 1589 Dihedral : 20.673 144.767 1939 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.18 % Allowed : 19.21 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1103 helix: 1.23 (0.29), residues: 334 sheet: -1.36 (0.29), residues: 283 loop : -1.49 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.005 0.001 HIS C 44 PHE 0.020 0.001 PHE D 68 TYR 0.010 0.001 TYR C 239 ARG 0.004 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 474) hydrogen bonds : angle 5.45033 ( 1306) covalent geometry : bond 0.00331 (10221) covalent geometry : angle 0.60993 (14067) *********************** 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 129 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.997 Fit side-chains REVERT: B 1 MET cc_start: 0.7410 (ppp) cc_final: 0.6916 (ptt) REVERT: B 90 LEU cc_start: 0.8957 (mm) cc_final: 0.8641 (mp) REVERT: A 75 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7403 (tmm) REVERT: A 108 GLN cc_start: 0.7997 (mp10) cc_final: 0.7737 (mp10) REVERT: A 131 GLN cc_start: 0.7970 (pm20) cc_final: 0.7561 (pm20) REVERT: C 68 MET cc_start: 0.8463 (pmm) cc_final: 0.8046 (pmm) REVERT: D 180 MET cc_start: 0.8428 (mmm) cc_final: 0.8062 (mpp) outliers start: 21 outliers final: 16 residues processed: 121 average time/residue: 0.1813 time to fit residues: 33.3278 Evaluate side-chains 118 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 64 LEU Chi-restraints excluded: chain D residue 101 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 72 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.147134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.117384 restraints weight = 16256.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.116984 restraints weight = 16456.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.118591 restraints weight = 17086.987| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10221 Z= 0.151 Angle : 0.618 12.830 14067 Z= 0.329 Chirality : 0.043 0.210 1619 Planarity : 0.004 0.062 1589 Dihedral : 20.669 144.812 1939 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.66 % Allowed : 20.04 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1103 helix: 1.25 (0.29), residues: 334 sheet: -1.28 (0.28), residues: 287 loop : -1.54 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.005 0.001 HIS D 63 PHE 0.020 0.001 PHE D 68 TYR 0.011 0.001 TYR C 239 ARG 0.003 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 474) hydrogen bonds : angle 5.43076 ( 1306) covalent geometry : bond 0.00351 (10221) covalent geometry : angle 0.61803 (14067) ********************** 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 121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.065 Fit side-chains REVERT: B 1 MET cc_start: 0.7441 (ppp) cc_final: 0.6961 (ptt) REVERT: B 90 LEU cc_start: 0.8984 (mm) cc_final: 0.8666 (mp) REVERT: A 75 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7394 (tmm) REVERT: A 131 GLN cc_start: 0.7967 (pm20) cc_final: 0.7548 (pm20) REVERT: C 68 MET cc_start: 0.8477 (pmm) cc_final: 0.8031 (pmm) outliers start: 16 outliers final: 13 residues processed: 115 average time/residue: 0.1893 time to fit residues: 33.8904 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 : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 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 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 101 SER Chi-restraints excluded: chain D residue 131 VAL 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 72 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.0030 chunk 104 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.145981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.116265 restraints weight = 16428.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.116103 restraints weight = 17565.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.117372 restraints weight = 20102.030| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10221 Z= 0.177 Angle : 0.640 12.477 14067 Z= 0.339 Chirality : 0.044 0.214 1619 Planarity : 0.004 0.062 1589 Dihedral : 20.693 144.611 1939 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.66 % Allowed : 20.15 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.25), residues: 1103 helix: 1.20 (0.29), residues: 334 sheet: -1.37 (0.29), residues: 284 loop : -1.53 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.003 0.001 HIS D 63 PHE 0.019 0.001 PHE D 68 TYR 0.013 0.002 TYR C 239 ARG 0.003 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 474) hydrogen bonds : angle 5.50960 ( 1306) covalent geometry : bond 0.00411 (10221) covalent geometry : angle 0.63988 (14067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3233.80 seconds wall clock time: 59 minutes 3.75 seconds (3543.75 seconds total)