Starting phenix.real_space_refine on Sat Dec 28 12:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y12_33554/12_2024/7y12_33554.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y12_33554/12_2024/7y12_33554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y12_33554/12_2024/7y12_33554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y12_33554/12_2024/7y12_33554.map" model { file = "/net/cci-nas-00/data/ceres_data/7y12_33554/12_2024/7y12_33554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y12_33554/12_2024/7y12_33554.cif" } resolution = 3.1 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5431 2.51 5 N 1454 2.21 5 O 1547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8501 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1654 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2053 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 253} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BAL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'PLM': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.69, per 1000 atoms: 0.67 Number of scatterers: 8501 At special positions: 0 Unit cell: (122.85, 84.375, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1547 8.00 N 1454 7.00 C 5431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL R1001 " Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.6% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 202 through 205 removed outlier: 4.038A pdb=" N ARG A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.158A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.503A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.537A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.686A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.583A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'R' and resid 23 through 52 Processing helix chain 'R' and resid 62 through 88 Processing helix chain 'R' and resid 92 through 129 removed outlier: 3.949A pdb=" N LYS R 96 " --> pdb=" O ASN R 92 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 140 through 165 Processing helix chain 'R' and resid 171 through 189 Processing helix chain 'R' and resid 189 through 209 removed outlier: 3.564A pdb=" N SER R 209 " --> pdb=" O VAL R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 234 Processing helix chain 'R' and resid 234 through 244 removed outlier: 3.983A pdb=" N SER R 238 " --> pdb=" O SER R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 247 No H-bonds generated for 'chain 'R' and resid 245 through 247' Processing helix chain 'R' and resid 253 through 277 Proline residue: R 273 - end of helix Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.925A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.408A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.651A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.802A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.987A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.690A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.701A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.507A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.551A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.596A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.929A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.929A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.915A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183 removed outlier: 6.752A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2292 1.33 - 1.45: 1585 1.45 - 1.57: 4699 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 8676 Sorted by residual: bond pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 1.247 1.306 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C1 PLM R1004 " pdb=" C2 PLM R1004 " ideal model delta sigma weight residual 1.542 1.508 0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 PLM R1003 " pdb=" C2 PLM R1003 " ideal model delta sigma weight residual 1.542 1.511 0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 PLM R1002 " pdb=" C2 PLM R1002 " ideal model delta sigma weight residual 1.542 1.512 0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C LEU R 235 " pdb=" N PRO R 236 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.00e+00 ... (remaining 8671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 11614 2.21 - 4.41: 122 4.41 - 6.62: 14 6.62 - 8.83: 5 8.83 - 11.04: 1 Bond angle restraints: 11756 Sorted by residual: angle pdb=" CA BAL R1001 " pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 120.80 113.33 7.47 1.70e+00 3.46e-01 1.93e+01 angle pdb=" CB MET R 42 " pdb=" CG MET R 42 " pdb=" SD MET R 42 " ideal model delta sigma weight residual 112.70 123.74 -11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CA MET R 42 " pdb=" CB MET R 42 " pdb=" CG MET R 42 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N BAL R1001 " pdb=" CB BAL R1001 " pdb=" CA BAL R1001 " ideal model delta sigma weight residual 110.40 114.96 -4.56 1.50e+00 4.44e-01 9.25e+00 angle pdb=" N MET R 42 " pdb=" CA MET R 42 " pdb=" CB MET R 42 " ideal model delta sigma weight residual 110.30 114.67 -4.37 1.54e+00 4.22e-01 8.03e+00 ... (remaining 11751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4517 17.97 - 35.93: 479 35.93 - 53.90: 110 53.90 - 71.86: 13 71.86 - 89.83: 12 Dihedral angle restraints: 5131 sinusoidal: 1912 harmonic: 3219 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 63.90 29.10 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA ASP B 303 " pdb=" CB ASP B 303 " pdb=" CG ASP B 303 " pdb=" OD1 ASP B 303 " ideal model delta sinusoidal sigma weight residual -30.00 -88.66 58.66 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N ARG B 52 " pdb=" CA ARG B 52 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 808 0.028 - 0.056: 355 0.056 - 0.085: 112 0.085 - 0.113: 67 0.113 - 0.141: 15 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1354 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.010 2.00e-02 2.50e+03 9.66e-03 1.87e+00 pdb=" CG TYR B 105 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO B 236 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 240 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C TYR R 240 " 0.023 2.00e-02 2.50e+03 pdb=" O TYR R 240 " -0.008 2.00e-02 2.50e+03 pdb=" N TRP R 241 " -0.008 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 124 2.65 - 3.21: 7641 3.21 - 3.77: 13387 3.77 - 4.34: 18365 4.34 - 4.90: 30773 Nonbonded interactions: 70290 Sorted by model distance: nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.086 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.147 3.040 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.187 3.120 nonbonded pdb=" OD1 ASN A 241 " pdb=" OH TYR A 287 " model vdw 2.213 3.040 nonbonded pdb=" O THR R 191 " pdb=" OG1 THR R 195 " model vdw 2.262 3.040 ... (remaining 70285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.240 Find NCS groups from input model: 0.100 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8676 Z= 0.223 Angle : 0.581 11.036 11756 Z= 0.295 Chirality : 0.040 0.141 1357 Planarity : 0.003 0.033 1468 Dihedral : 15.813 89.828 3043 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.22 % Allowed : 15.96 % Favored : 83.82 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.86 (0.27), residues: 1093 helix: 2.18 (0.28), residues: 361 sheet: -0.05 (0.32), residues: 271 loop : -0.27 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.003 0.001 HIS B 142 PHE 0.019 0.001 PHE R 75 TYR 0.024 0.002 TYR B 105 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.998 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 145 average time/residue: 0.2212 time to fit residues: 44.2025 Evaluate side-chains 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 262 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 0.0000 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8676 Z= 0.155 Angle : 0.501 5.625 11756 Z= 0.272 Chirality : 0.040 0.155 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.543 50.898 1242 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.69 % Allowed : 15.51 % Favored : 82.81 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 1.09 (0.27), residues: 1093 helix: 2.35 (0.28), residues: 380 sheet: -0.00 (0.32), residues: 266 loop : -0.17 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE R 75 TYR 0.012 0.001 TYR B 105 ARG 0.003 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.979 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 161 average time/residue: 0.2046 time to fit residues: 45.8880 Evaluate side-chains 151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.195 Angle : 0.510 7.275 11756 Z= 0.274 Chirality : 0.041 0.154 1357 Planarity : 0.003 0.032 1468 Dihedral : 5.446 52.731 1239 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.58 % Allowed : 16.63 % Favored : 80.79 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 1.02 (0.26), residues: 1093 helix: 2.35 (0.27), residues: 380 sheet: -0.04 (0.32), residues: 263 loop : -0.26 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 144 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.001 PHE R 75 TYR 0.015 0.002 TYR B 105 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.992 Fit side-chains REVERT: A 5 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7359 (mp) outliers start: 23 outliers final: 15 residues processed: 163 average time/residue: 0.2054 time to fit residues: 46.8238 Evaluate side-chains 158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN R 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 8676 Z= 0.519 Angle : 0.727 9.656 11756 Z= 0.386 Chirality : 0.049 0.204 1357 Planarity : 0.005 0.039 1468 Dihedral : 7.389 58.539 1239 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.48 % Allowed : 18.31 % Favored : 78.20 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.10 (0.25), residues: 1093 helix: 1.46 (0.27), residues: 368 sheet: -0.26 (0.32), residues: 252 loop : -0.80 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP R 144 HIS 0.006 0.002 HIS B 142 PHE 0.029 0.003 PHE R 75 TYR 0.026 0.003 TYR B 105 ARG 0.005 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.050 Fit side-chains REVERT: A 5 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7575 (mp) REVERT: B 134 ARG cc_start: 0.7183 (ttp80) cc_final: 0.6641 (ttp-110) REVERT: B 340 ASN cc_start: 0.8094 (t0) cc_final: 0.7813 (t0) outliers start: 31 outliers final: 21 residues processed: 155 average time/residue: 0.2200 time to fit residues: 46.7829 Evaluate side-chains 153 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0870 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 0.0570 chunk 77 optimal weight: 0.0030 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8676 Z= 0.136 Angle : 0.502 8.063 11756 Z= 0.265 Chirality : 0.039 0.152 1357 Planarity : 0.003 0.036 1468 Dihedral : 5.861 58.135 1239 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.70 % Allowed : 19.55 % Favored : 77.75 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.80 (0.26), residues: 1093 helix: 2.32 (0.27), residues: 375 sheet: -0.21 (0.32), residues: 263 loop : -0.48 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 144 HIS 0.003 0.000 HIS S 35 PHE 0.012 0.001 PHE R 75 TYR 0.010 0.001 TYR S 60 ARG 0.002 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: R 156 MET cc_start: 0.7783 (mmm) cc_final: 0.7491 (mmt) outliers start: 24 outliers final: 15 residues processed: 164 average time/residue: 0.1984 time to fit residues: 45.6035 Evaluate side-chains 158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8676 Z= 0.162 Angle : 0.503 7.675 11756 Z= 0.266 Chirality : 0.040 0.139 1357 Planarity : 0.003 0.035 1468 Dihedral : 5.469 57.873 1239 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.03 % Allowed : 20.45 % Favored : 76.52 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.89 (0.26), residues: 1093 helix: 2.37 (0.27), residues: 377 sheet: -0.12 (0.32), residues: 263 loop : -0.45 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.020 0.001 PHE S 68 TYR 0.010 0.001 TYR B 105 ARG 0.002 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7418 (mp) REVERT: R 156 MET cc_start: 0.7775 (mmm) cc_final: 0.7493 (mmt) REVERT: S 113 GLN cc_start: 0.6687 (mm-40) cc_final: 0.6340 (mm-40) outliers start: 27 outliers final: 19 residues processed: 170 average time/residue: 0.1956 time to fit residues: 46.6749 Evaluate side-chains 158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8676 Z= 0.211 Angle : 0.535 7.188 11756 Z= 0.283 Chirality : 0.041 0.149 1357 Planarity : 0.003 0.035 1468 Dihedral : 5.663 55.974 1239 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.71 % Allowed : 19.78 % Favored : 76.52 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.81 (0.26), residues: 1093 helix: 2.26 (0.27), residues: 377 sheet: -0.12 (0.32), residues: 263 loop : -0.49 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 144 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.002 PHE R 75 TYR 0.013 0.002 TYR B 105 ARG 0.005 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7369 (mp) REVERT: B 134 ARG cc_start: 0.7141 (ttp80) cc_final: 0.6707 (ttp-110) REVERT: R 156 MET cc_start: 0.7774 (mmm) cc_final: 0.7505 (mmt) REVERT: S 113 GLN cc_start: 0.6751 (mm-40) cc_final: 0.6447 (mm-40) outliers start: 33 outliers final: 25 residues processed: 166 average time/residue: 0.2049 time to fit residues: 47.5850 Evaluate side-chains 167 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 0.0000 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 0.0470 overall best weight: 0.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8676 Z= 0.131 Angle : 0.492 8.240 11756 Z= 0.258 Chirality : 0.039 0.148 1357 Planarity : 0.003 0.035 1468 Dihedral : 5.088 57.576 1239 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.81 % Allowed : 20.67 % Favored : 76.52 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.99 (0.27), residues: 1093 helix: 2.47 (0.28), residues: 379 sheet: -0.05 (0.32), residues: 263 loop : -0.45 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 144 HIS 0.003 0.000 HIS S 35 PHE 0.016 0.001 PHE R 75 TYR 0.008 0.001 TYR S 94 ARG 0.003 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7296 (mp) REVERT: R 156 MET cc_start: 0.7794 (mmm) cc_final: 0.7526 (mmt) REVERT: S 113 GLN cc_start: 0.6665 (mm-40) cc_final: 0.6432 (mm-40) outliers start: 25 outliers final: 22 residues processed: 164 average time/residue: 0.1972 time to fit residues: 45.6728 Evaluate side-chains 163 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.183 Angle : 0.518 7.692 11756 Z= 0.272 Chirality : 0.040 0.140 1357 Planarity : 0.003 0.035 1468 Dihedral : 5.314 54.598 1239 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.15 % Allowed : 20.56 % Favored : 76.29 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.93 (0.26), residues: 1093 helix: 2.39 (0.27), residues: 378 sheet: -0.04 (0.32), residues: 263 loop : -0.47 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 75 TYR 0.012 0.002 TYR A 320 ARG 0.004 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7353 (mp) REVERT: R 156 MET cc_start: 0.7790 (mmm) cc_final: 0.7529 (mmt) REVERT: S 47 TRP cc_start: 0.7504 (t60) cc_final: 0.7229 (t60) REVERT: S 113 GLN cc_start: 0.6684 (mm-40) cc_final: 0.6461 (mm-40) outliers start: 28 outliers final: 25 residues processed: 164 average time/residue: 0.1960 time to fit residues: 45.5931 Evaluate side-chains 164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 107 optimal weight: 0.4980 chunk 99 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.188 Angle : 0.526 8.367 11756 Z= 0.276 Chirality : 0.041 0.142 1357 Planarity : 0.003 0.035 1468 Dihedral : 5.413 55.137 1239 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.92 % Allowed : 20.90 % Favored : 76.18 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.89 (0.26), residues: 1093 helix: 2.36 (0.27), residues: 377 sheet: -0.06 (0.32), residues: 265 loop : -0.48 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 75 TYR 0.011 0.002 TYR B 105 ARG 0.004 0.000 ARG S 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7378 (mp) REVERT: B 340 ASN cc_start: 0.7873 (t0) cc_final: 0.7586 (t0) REVERT: S 113 GLN cc_start: 0.6735 (mm-40) cc_final: 0.6495 (mm-40) outliers start: 26 outliers final: 24 residues processed: 159 average time/residue: 0.1912 time to fit residues: 42.8756 Evaluate side-chains 164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.0060 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.172003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138323 restraints weight = 10323.973| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.03 r_work: 0.3428 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8676 Z= 0.176 Angle : 0.518 8.101 11756 Z= 0.272 Chirality : 0.040 0.140 1357 Planarity : 0.003 0.035 1468 Dihedral : 5.344 55.477 1239 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.92 % Allowed : 20.56 % Favored : 76.52 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.92 (0.26), residues: 1093 helix: 2.41 (0.27), residues: 377 sheet: -0.06 (0.32), residues: 265 loop : -0.48 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE R 75 TYR 0.010 0.001 TYR B 105 ARG 0.004 0.000 ARG S 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2153.60 seconds wall clock time: 40 minutes 9.20 seconds (2409.20 seconds total)