Starting phenix.real_space_refine on Wed Aug 5 01:40:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w2w_65582/08_2026/9w2w_65582_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w2w_65582/08_2026/9w2w_65582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w2w_65582/08_2026/9w2w_65582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w2w_65582/08_2026/9w2w_65582.map" model { file = "/net/cci-nas-00/data/ceres_data/9w2w_65582/08_2026/9w2w_65582_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w2w_65582/08_2026/9w2w_65582_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 4963 2.51 5 N 1448 2.21 5 O 1472 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7905 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2520 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 15, 'TRANS': 383} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 558 Unresolved non-hydrogen angles: 721 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'PHE:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 12, 'ASP:plan': 10, 'GLU:plan': 6, 'GLN:plan1': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 213 Chain: "D" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1406 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 6, 'TRANS': 216} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 12, 'HIS:plan': 3, 'PHE:plan': 2, 'ASP:plan': 12, 'GLN:plan1': 8, 'ASN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 175 Chain: "B" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 2526 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 15, 'TRANS': 384} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 564 Unresolved non-hydrogen angles: 733 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'PHE:plan': 8, 'ARG:plan': 8, 'ASN:plan1': 11, 'ASP:plan': 10, 'GLU:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 213 Chain: "C" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1397 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 6, 'TRANS': 216} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 349 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 13, 'HIS:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 9, 'ASN:plan1': 1, 'TYR:plan': 3, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 211 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'R6Q': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'R6Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.07, per 1000 atoms: 0.26 Number of scatterers: 7905 At special positions: 0 Unit cell: (86.835, 65.333, 138.936, 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 16 16.00 F 6 9.00 O 1472 8.00 N 1448 7.00 C 4963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 517.5 milliseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 55.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 20 through 63 removed outlier: 3.878A pdb=" N SER A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.811A pdb=" N LEU A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 253 through 297 removed outlier: 7.257A pdb=" N ASN A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 310 through 355 removed outlier: 4.942A pdb=" N SER A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASP A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 392 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 103 through 114 Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 119 through 135 Processing helix chain 'D' and resid 148 through 163 removed outlier: 4.455A pdb=" N THR D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 197 Processing helix chain 'D' and resid 207 through 211 Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 21 through 63 removed outlier: 3.799A pdb=" N VAL B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.537A pdb=" N LEU B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 206 through 214 Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 258 through 297 removed outlier: 3.665A pdb=" N ASN B 262 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 310 through 355 removed outlier: 4.860A pdb=" N SER B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 392 Processing helix chain 'B' and resid 393 through 402 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 77 through 89 Processing helix chain 'C' and resid 103 through 114 Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 119 through 135 Processing helix chain 'C' and resid 148 through 163 removed outlier: 4.423A pdb=" N THR C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 197 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.531A pdb=" N VAL A 189 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 149 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 191 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY A 150 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL A 202 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 205 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA4, first strand: chain 'D' and resid 30 through 33 removed outlier: 3.606A pdb=" N GLN D 71 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.806A pdb=" N LYS D 13 " --> pdb=" O VAL D 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 38 through 41 removed outlier: 3.672A pdb=" N VAL D 41 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 222 through 227 removed outlier: 3.740A pdb=" N LYS B 184 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 182 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR B 204 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 205 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 33 removed outlier: 3.686A pdb=" N GLN C 71 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 17 removed outlier: 6.585A pdb=" N LYS C 13 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C 17 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.596A pdb=" N VAL C 41 " --> pdb=" O LEU C 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.153A pdb=" N GLY C 90 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASP C 171 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL C 92 " --> pdb=" O ASP C 171 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1668 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: 1.42 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1361 1.31 - 1.43: 2035 1.43 - 1.56: 4581 1.56 - 1.68: 10 1.68 - 1.80: 32 Bond restraints: 8019 Sorted by residual: bond pdb=" C03 R6Q A 501 " pdb=" C04 R6Q A 501 " ideal model delta sigma weight residual 1.386 1.194 0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" C03 R6Q B 501 " pdb=" C04 R6Q B 501 " ideal model delta sigma weight residual 1.386 1.194 0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" C01 R6Q A 501 " pdb=" C06 R6Q A 501 " ideal model delta sigma weight residual 1.387 1.564 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" C01 R6Q B 501 " pdb=" C06 R6Q B 501 " ideal model delta sigma weight residual 1.387 1.563 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" C04 R6Q A 501 " pdb=" C05 R6Q A 501 " ideal model delta sigma weight residual 1.389 1.215 0.174 2.00e-02 2.50e+03 7.58e+01 ... (remaining 8014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 10954 3.03 - 6.07: 35 6.07 - 9.10: 2 9.10 - 12.13: 3 12.13 - 15.16: 5 Bond angle restraints: 10999 Sorted by residual: angle pdb=" C03 R6Q A 501 " pdb=" C04 R6Q A 501 " pdb=" C05 R6Q A 501 " ideal model delta sigma weight residual 119.42 134.58 -15.16 3.00e+00 1.11e-01 2.55e+01 angle pdb=" C03 R6Q B 501 " pdb=" C04 R6Q B 501 " pdb=" C05 R6Q B 501 " ideal model delta sigma weight residual 119.42 134.54 -15.12 3.00e+00 1.11e-01 2.54e+01 angle pdb=" C15 R6Q A 501 " pdb=" C10 R6Q A 501 " pdb=" O09 R6Q A 501 " ideal model delta sigma weight residual 104.77 91.38 13.39 3.00e+00 1.11e-01 1.99e+01 angle pdb=" C15 R6Q B 501 " pdb=" C10 R6Q B 501 " pdb=" O09 R6Q B 501 " ideal model delta sigma weight residual 104.77 91.62 13.15 3.00e+00 1.11e-01 1.92e+01 angle pdb=" C02 R6Q B 501 " pdb=" C01 R6Q B 501 " pdb=" C06 R6Q B 501 " ideal model delta sigma weight residual 120.73 108.56 12.17 3.00e+00 1.11e-01 1.65e+01 ... (remaining 10994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.64: 4377 25.64 - 51.28: 239 51.28 - 76.91: 22 76.91 - 102.55: 6 102.55 - 128.19: 2 Dihedral angle restraints: 4646 sinusoidal: 1092 harmonic: 3554 Sorted by residual: dihedral pdb=" C10 R6Q A 501 " pdb=" C14 R6Q A 501 " pdb=" C15 R6Q A 501 " pdb=" N13 R6Q A 501 " ideal model delta sinusoidal sigma weight residual -56.48 71.71 -128.19 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C10 R6Q B 501 " pdb=" C14 R6Q B 501 " pdb=" C15 R6Q B 501 " pdb=" N13 R6Q B 501 " ideal model delta sinusoidal sigma weight residual -56.48 70.74 -127.22 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" C12 R6Q B 501 " pdb=" C14 R6Q B 501 " pdb=" N13 R6Q B 501 " pdb=" C15 R6Q B 501 " ideal model delta sinusoidal sigma weight residual 59.37 -39.43 98.80 1 3.00e+01 1.11e-03 1.23e+01 ... (remaining 4643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 817 0.025 - 0.050: 258 0.050 - 0.075: 169 0.075 - 0.100: 86 0.100 - 0.125: 26 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA PRO B 88 " pdb=" N PRO B 88 " pdb=" C PRO B 88 " pdb=" CB PRO B 88 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL C 92 " pdb=" N VAL C 92 " pdb=" C VAL C 92 " pdb=" CB VAL C 92 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA VAL D 92 " pdb=" N VAL D 92 " pdb=" C VAL D 92 " pdb=" CB VAL D 92 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 1353 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 261 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C PHE B 261 " 0.067 2.00e-02 2.50e+03 pdb=" O PHE B 261 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN B 262 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 57 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ASN B 57 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN B 57 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG B 58 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 57 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ASN A 57 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 57 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 58 " -0.011 2.00e-02 2.50e+03 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1662 2.77 - 3.31: 7970 3.31 - 3.84: 12916 3.84 - 4.37: 13439 4.37 - 4.90: 24698 Nonbonded interactions: 60685 Sorted by model distance: nonbonded pdb=" O SER A 211 " pdb=" N LEU A 216 " model vdw 2.243 3.120 nonbonded pdb=" O SER C 49 " pdb=" ND1 HIS C 53 " model vdw 2.319 3.120 nonbonded pdb=" O THR A 104 " pdb=" OG1 THR A 104 " model vdw 2.328 3.040 nonbonded pdb=" O ALA A 341 " pdb=" OG SER A 370 " model vdw 2.439 3.040 nonbonded pdb=" OH TYR A 363 " pdb=" OE2 GLU B 267 " model vdw 2.451 3.040 ... (remaining 60680 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 1 through 29 or (resid 30 through 32 and (name N or name C \ A or name C or name O or name CB )) or resid 33 or (resid 34 through 35 and (nam \ e N or name CA or name C or name O or name CB )) or resid 36 through 54 or (resi \ d 55 through 56 and (name N or name CA or name C or name O or name CB )) or resi \ d 57 through 82 or (resid 83 through 85 and (name N or name CA or name C or name \ O or name CB )) or resid 86 through 88 or (resid 89 through 90 and (name N or n \ ame CA or name C or name O or name CB )) or resid 91 through 95 or (resid 96 and \ (name N or name CA or name C or name O or name CB )) or resid 97 through 102 or \ (resid 103 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 4 through 116 or (resid 117 and (name N or name CA or name C or name O or name C \ B )) or resid 118 through 135 or (resid 136 through 142 and (name N or name CA o \ r name C or name O or name CB )) or (resid 143 through 145 and (name N or name C \ A or name C or name O or name CB )) or (resid 146 through 149 and (name N or nam \ e CA or name C or name O or name CB )) or resid 150 through 163 or (resid 164 th \ rough 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ through 184 or (resid 185 and (name N or name CA or name C or name O or name CB \ )) or resid 186 through 188 or (resid 189 and (name N or name CA or name C or na \ me O or name CB )) or resid 190 through 198 or (resid 199 and (name N or name CA \ or name C or name O or name CB )) or resid 200 through 222 or (resid 223 throug \ h 224 and (name N or name CA or name C or name O or name CB )) or resid 225 thro \ ugh 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) o \ r resid 239 through 250 or (resid 251 through 252 and (name N or name CA or name \ C or name O or name CB )) or resid 253 through 264 or (resid 265 through 266 an \ d (name N or name CA or name C or name O or name CB )) or resid 267 through 268 \ or (resid 269 and (name N or name CA or name C or name O or name CB )) or resid \ 270 through 343 or (resid 344 and (name N or name CA or name C or name O or name \ CB )) or resid 345 through 366 or (resid 367 and (name N or name CA or name C o \ r name O or name CB )) or resid 368 or (resid 369 and (name N or name CA or name \ C or name O or name CB )) or resid 370 through 374 or (resid 375 through 376 an \ d (name N or name CA or name C or name O or name CB )) or resid 377 or (resid 37 \ 8 through 381 and (name N or name CA or name C or name O or name CB )) or resid \ 382 through 401 or (resid 402 through 408 and (name N or name CA or name C or na \ me O or name CB )) or resid 501)) selection = (chain 'B' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 24 or (resid 25 through 32 and (name \ N or name CA or name C or name O or name CB )) or resid 33 through 39 or (resid \ 40 through 41 and (name N or name CA or name C or name O or name CB )) or resid \ 42 through 55 or (resid 56 and (name N or name CA or name C or name O or name C \ B )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or name \ CB )) or resid 59 through 70 or (resid 71 through 74 and (name N or name CA or \ name C or name O or name CB )) or resid 75 through 84 or (resid 85 and (name N o \ r name CA or name C or name O or name CB )) or resid 86 through 121 or (resid 12 \ 2 through 124 and (name N or name CA or name C or name O or name CB )) or resid \ 125 through 131 or (resid 132 through 134 and (name N or name CA or name C or na \ me O or name CB )) or (resid 135 through 145 and (name N or name CA or name C or \ name O or name CB )) or resid 146 through 168 or (resid 169 through 170 and (na \ me N or name CA or name C or name O or name CB )) or (resid 180 through 185 and \ (name N or name CA or name C or name O or name CB )) or resid 186 or (resid 187 \ and (name N or name CA or name C or name O or name CB )) or resid 188 through 21 \ 0 or (resid 211 through 216 and (name N or name CA or name C or name O or name C \ B )) or resid 217 or (resid 218 and (name N or name CA or name C or name O or na \ me CB )) or resid 219 through 242 or (resid 243 through 245 and (name N or name \ CA or name C or name O or name CB )) or resid 246 through 254 or (resid 255 and \ (name N or name CA or name C or name O or name CB )) or resid 256 through 287 or \ (resid 288 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 9 through 314 or (resid 315 and (name N or name CA or name C or name O or name C \ B )) or resid 316 through 324 or (resid 325 and (name N or name CA or name C or \ name O or name CB )) or resid 326 through 334 or (resid 335 through 336 and (nam \ e N or name CA or name C or name O or name CB )) or resid 337 through 338 or (re \ sid 339 and (name N or name CA or name C or name O or name CB )) or resid 340 th \ rough 342 or (resid 343 through 344 and (name N or name CA or name C or name O o \ r name CB )) or resid 345 through 354 or (resid 355 and (name N or name CA or na \ me C or name O or name CB )) or resid 356 through 375 or (resid 376 and (name N \ or name CA or name C or name O or name CB )) or resid 377 through 383 or (resid \ 384 through 385 and (name N or name CA or name C or name O or name CB )) or resi \ d 386 through 387 or (resid 388 and (name N or name CA or name C or name O or na \ me CB )) or resid 389 through 397 or (resid 398 through 400 and (name N or name \ CA or name C or name O or name CB )) or resid 401 through 402 or (resid 403 thro \ ugh 408 and (name N or name CA or name C or name O or name CB )) or resid 501)) } ncs_group { reference = (chain 'C' and ((resid 3 through 11 and (name N or name CA or name C or name O o \ r name CB )) or resid 12 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 or (resid 24 through 26 and (name N or nam \ e CA or name C or name O or name CB )) or resid 27 through 43 or (resid 44 and ( \ name N or name CA or name C or name O or name CB )) or resid 45 through 111 or ( \ resid 112 through 113 and (name N or name CA or name C or name O or name CB )) o \ r resid 114 through 136 or (resid 137 through 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 156 or (resid 157 through 158 an \ d (name N or name CA or name C or name O or name CB )) or resid 159 through 160 \ or (resid 161 and (name N or name CA or name C or name O or name CB )) or resid \ 162 through 188 or (resid 189 through 203 and (name N or name CA or name C or na \ me O or name CB )) or resid 204 through 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 225)) selection = (chain 'D' and ((resid 3 through 11 and (name N or name CA or name C or name O o \ r name CB )) or resid 12 through 24 or (resid 25 through 26 and (name N or name \ CA or name C or name O or name CB )) or (resid 27 through 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 31 or (resid 32 throug \ h 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throug \ h 48 or (resid 49 and (name N or name CA or name C or name O or name CB )) or re \ sid 50 through 83 or (resid 84 and (name N or name CA or name C or name O or nam \ e CB )) or resid 85 through 119 or (resid 120 through 122 and (name N or name CA \ or name C or name O or name CB )) or resid 123 through 145 or (resid 146 throug \ h 147 and (name N or name CA or name C or name O or name CB )) or resid 148 thro \ ugh 153 or (resid 154 through 158 and (name N or name CA or name C or name O or \ name CB )) or resid 159 through 171 or (resid 172 and (name N or name CA or name \ C or name O or name CB )) or resid 173 through 223 or (resid 224 and (name N or \ name CA or name C or name O or name CB )) or resid 225)) } 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.500 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.008 0.192 8019 Z= 0.408 Angle : 0.645 15.164 10999 Z= 0.361 Chirality : 0.039 0.125 1356 Planarity : 0.003 0.040 1453 Dihedral : 15.941 128.190 2352 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.95 % Favored : 94.81 % Rotamer: Outliers : 0.20 % Allowed : 32.48 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 1233 helix: 2.78 (0.21), residues: 647 sheet: -2.92 (0.36), residues: 183 loop : -1.83 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 53 TYR 0.012 0.001 TYR A 371 PHE 0.015 0.001 PHE B 25 TRP 0.010 0.001 TRP B 350 HIS 0.006 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.41 ( 8019) covalent geometry : angle 0.64515 / 0.36 (10999) hydrogen bonds : bond 0.14006 / 10.23 ( 584) hydrogen bonds : angle 6.27445 / 4.58 ( 1668) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.283 Fit side-chains REVERT: A 67 THR cc_start: 0.9297 (t) cc_final: 0.9068 (m) REVERT: A 108 GLN cc_start: 0.7466 (mp10) cc_final: 0.7165 (mt0) REVERT: A 185 ARG cc_start: 0.7958 (ptm-80) cc_final: 0.7745 (ttp80) REVERT: B 151 LYS cc_start: 0.8301 (tttt) cc_final: 0.8098 (tttm) REVERT: C 9 LYS cc_start: 0.8676 (mptt) cc_final: 0.8210 (mttt) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.0829 time to fit residues: 13.6872 Evaluate side-chains 113 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.146862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.123989 restraints weight = 10033.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125690 restraints weight = 6932.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.127041 restraints weight = 5455.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.127673 restraints weight = 4697.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127758 restraints weight = 4295.060| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8019 Z= 0.111 Angle : 0.466 7.165 10999 Z= 0.253 Chirality : 0.041 0.130 1356 Planarity : 0.003 0.040 1453 Dihedral : 5.649 99.443 1321 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.62 % Favored : 95.13 % Rotamer: Outliers : 2.95 % Allowed : 28.15 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1233 helix: 2.66 (0.21), residues: 658 sheet: -2.70 (0.34), residues: 189 loop : -1.51 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 373 TYR 0.016 0.001 TYR A 371 PHE 0.021 0.001 PHE B 318 TRP 0.007 0.001 TRP B 350 HIS 0.003 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 ( 8019) covalent geometry : angle 0.46601 / 0.25 (10999) hydrogen bonds : bond 0.03682 / 2.70 ( 584) hydrogen bonds : angle 4.66801 / 3.44 ( 1668) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.289 Fit side-chains REVERT: A 108 GLN cc_start: 0.7136 (mp10) cc_final: 0.6856 (mt0) REVERT: A 117 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7462 (pp) REVERT: C 9 LYS cc_start: 0.8369 (mptt) cc_final: 0.8154 (mttm) outliers start: 15 outliers final: 11 residues processed: 124 average time/residue: 0.0786 time to fit residues: 13.9446 Evaluate side-chains 122 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 28 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 86 ASN A 262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.144354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121517 restraints weight = 10073.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.122983 restraints weight = 7097.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.124259 restraints weight = 5665.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.125216 restraints weight = 4848.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.125410 restraints weight = 4444.173| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8019 Z= 0.190 Angle : 0.525 5.822 10999 Z= 0.289 Chirality : 0.043 0.139 1356 Planarity : 0.004 0.041 1453 Dihedral : 6.291 97.364 1321 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.52 % Favored : 94.32 % Rotamer: Outliers : 5.12 % Allowed : 26.18 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1233 helix: 2.27 (0.20), residues: 646 sheet: -2.47 (0.33), residues: 199 loop : -1.52 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 373 TYR 0.021 0.002 TYR A 371 PHE 0.024 0.002 PHE B 318 TRP 0.006 0.001 TRP D 224 HIS 0.006 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 8019) covalent geometry : angle 0.52505 / 0.29 (10999) hydrogen bonds : bond 0.04449 / 3.27 ( 584) hydrogen bonds : angle 4.75086 / 3.49 ( 1668) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.294 Fit side-chains REVERT: A 13 TYR cc_start: 0.8664 (m-10) cc_final: 0.8397 (m-10) REVERT: A 96 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8134 (p90) REVERT: A 117 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7523 (pp) REVERT: A 189 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8600 (p) REVERT: C 9 LYS cc_start: 0.8339 (mptt) cc_final: 0.8055 (mttm) outliers start: 26 outliers final: 14 residues processed: 138 average time/residue: 0.0791 time to fit residues: 15.4897 Evaluate side-chains 132 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 218 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 GLN C 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.149256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126615 restraints weight = 10149.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128411 restraints weight = 6944.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.129861 restraints weight = 5411.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.130375 restraints weight = 4615.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.131325 restraints weight = 4243.473| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8019 Z= 0.098 Angle : 0.429 5.679 10999 Z= 0.235 Chirality : 0.041 0.127 1356 Planarity : 0.003 0.038 1453 Dihedral : 5.343 92.137 1321 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.62 % Favored : 95.13 % Rotamer: Outliers : 3.74 % Allowed : 26.57 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1233 helix: 2.46 (0.20), residues: 659 sheet: -2.24 (0.34), residues: 198 loop : -1.56 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 373 TYR 0.013 0.001 TYR A 371 PHE 0.015 0.001 PHE B 318 TRP 0.007 0.001 TRP D 224 HIS 0.002 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 ( 8019) covalent geometry : angle 0.42915 / 0.23 (10999) hydrogen bonds : bond 0.03394 / 2.49 ( 584) hydrogen bonds : angle 4.22716 / 3.14 ( 1668) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 117 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7575 (pp) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.0823 time to fit residues: 14.7347 Evaluate side-chains 126 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 218 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 108 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.147744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123968 restraints weight = 10330.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126055 restraints weight = 6914.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127570 restraints weight = 5370.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.128254 restraints weight = 4573.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128891 restraints weight = 4163.308| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8019 Z= 0.102 Angle : 0.431 6.282 10999 Z= 0.235 Chirality : 0.041 0.245 1356 Planarity : 0.003 0.038 1453 Dihedral : 5.329 95.767 1321 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.62 % Favored : 95.13 % Rotamer: Outliers : 4.53 % Allowed : 27.17 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1233 helix: 2.54 (0.20), residues: 659 sheet: -2.09 (0.35), residues: 197 loop : -1.49 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 224 TYR 0.012 0.001 TYR A 371 PHE 0.018 0.001 PHE B 25 TRP 0.006 0.001 TRP D 224 HIS 0.002 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 ( 8019) covalent geometry : angle 0.43130 / 0.23 (10999) hydrogen bonds : bond 0.03382 / 2.49 ( 584) hydrogen bonds : angle 4.12427 / 3.06 ( 1668) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.294 Fit side-chains REVERT: A 67 THR cc_start: 0.9255 (t) cc_final: 0.8937 (m) REVERT: A 117 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7505 (pp) REVERT: A 151 LYS cc_start: 0.8338 (ttpt) cc_final: 0.7960 (tttm) outliers start: 23 outliers final: 20 residues processed: 124 average time/residue: 0.0763 time to fit residues: 13.6878 Evaluate side-chains 129 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 218 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.147291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124559 restraints weight = 10187.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126236 restraints weight = 7203.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127656 restraints weight = 5722.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128584 restraints weight = 4950.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128921 restraints weight = 4462.523| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8019 Z= 0.162 Angle : 0.485 5.342 10999 Z= 0.266 Chirality : 0.043 0.272 1356 Planarity : 0.003 0.040 1453 Dihedral : 5.853 92.958 1321 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.52 % Favored : 94.24 % Rotamer: Outliers : 5.71 % Allowed : 26.77 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1233 helix: 2.43 (0.20), residues: 646 sheet: -1.98 (0.35), residues: 197 loop : -1.42 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 224 TYR 0.016 0.001 TYR A 371 PHE 0.021 0.002 PHE B 318 TRP 0.005 0.001 TRP A 77 HIS 0.004 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 8019) covalent geometry : angle 0.48453 / 0.27 (10999) hydrogen bonds : bond 0.04030 / 2.97 ( 584) hydrogen bonds : angle 4.43314 / 3.27 ( 1668) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.307 Fit side-chains REVERT: A 13 TYR cc_start: 0.8645 (m-10) cc_final: 0.8422 (m-10) REVERT: A 67 THR cc_start: 0.9280 (t) cc_final: 0.8975 (m) REVERT: A 117 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7543 (pp) REVERT: A 151 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8034 (tttm) outliers start: 29 outliers final: 25 residues processed: 134 average time/residue: 0.0762 time to fit residues: 14.7066 Evaluate side-chains 137 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 218 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 120 optimal weight: 0.0170 chunk 59 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.152008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129612 restraints weight = 10240.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131520 restraints weight = 6968.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132803 restraints weight = 5447.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133806 restraints weight = 4608.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134017 restraints weight = 4185.338| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8019 Z= 0.091 Angle : 0.414 5.164 10999 Z= 0.228 Chirality : 0.041 0.262 1356 Planarity : 0.003 0.038 1453 Dihedral : 5.223 93.101 1321 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.79 % Favored : 94.97 % Rotamer: Outliers : 4.13 % Allowed : 28.15 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.25), residues: 1233 helix: 2.59 (0.20), residues: 659 sheet: -1.89 (0.36), residues: 193 loop : -1.48 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.009 0.001 TYR A 371 PHE 0.013 0.001 PHE B 318 TRP 0.006 0.001 TRP D 224 HIS 0.002 0.000 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.09 ( 8019) covalent geometry : angle 0.41366 / 0.23 (10999) hydrogen bonds : bond 0.03225 / 2.37 ( 584) hydrogen bonds : angle 4.02570 / 3.00 ( 1668) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.308 Fit side-chains REVERT: A 117 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7462 (pp) REVERT: A 151 LYS cc_start: 0.8307 (ttpt) cc_final: 0.7917 (tttm) outliers start: 21 outliers final: 19 residues processed: 128 average time/residue: 0.0774 time to fit residues: 14.3782 Evaluate side-chains 128 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 218 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 0.0470 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 0.0270 chunk 82 optimal weight: 5.9990 chunk 30 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.154323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131236 restraints weight = 10268.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133470 restraints weight = 6880.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.134957 restraints weight = 5266.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.135626 restraints weight = 4458.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.135689 restraints weight = 4068.959| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.022 8019 Z= 0.077 Angle : 0.396 6.505 10999 Z= 0.216 Chirality : 0.041 0.266 1356 Planarity : 0.003 0.036 1453 Dihedral : 4.651 87.810 1321 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.30 % Favored : 95.46 % Rotamer: Outliers : 2.36 % Allowed : 30.51 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1233 helix: 2.89 (0.20), residues: 660 sheet: -1.74 (0.36), residues: 199 loop : -1.26 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 373 TYR 0.005 0.000 TYR B 8 PHE 0.026 0.001 PHE B 25 TRP 0.006 0.001 TRP D 224 HIS 0.002 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00137 / 0.08 ( 8019) covalent geometry : angle 0.39641 / 0.22 (10999) hydrogen bonds : bond 0.02790 / 2.06 ( 584) hydrogen bonds : angle 3.67267 / 2.76 ( 1668) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.303 Fit side-chains REVERT: A 117 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7294 (pp) REVERT: A 151 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7829 (tttm) outliers start: 12 outliers final: 8 residues processed: 122 average time/residue: 0.0773 time to fit residues: 13.5819 Evaluate side-chains 118 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 259 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.0050 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.151569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.129712 restraints weight = 10148.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.129953 restraints weight = 8782.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.130286 restraints weight = 8056.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.130538 restraints weight = 7298.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131010 restraints weight = 6333.841| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8019 Z= 0.084 Angle : 0.413 5.673 10999 Z= 0.224 Chirality : 0.041 0.276 1356 Planarity : 0.003 0.036 1453 Dihedral : 4.731 86.477 1321 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.79 % Favored : 95.05 % Rotamer: Outliers : 2.76 % Allowed : 29.72 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1233 helix: 2.90 (0.20), residues: 660 sheet: -1.61 (0.36), residues: 199 loop : -1.21 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.007 0.001 TYR A 371 PHE 0.020 0.001 PHE B 25 TRP 0.006 0.001 TRP D 224 HIS 0.002 0.000 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00157 / 0.08 ( 8019) covalent geometry : angle 0.41321 / 0.22 (10999) hydrogen bonds : bond 0.02941 / 2.17 ( 584) hydrogen bonds : angle 3.69007 / 2.75 ( 1668) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.297 Fit side-chains REVERT: A 117 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7518 (pp) REVERT: A 151 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7908 (tttm) outliers start: 14 outliers final: 11 residues processed: 117 average time/residue: 0.0783 time to fit residues: 13.1924 Evaluate side-chains 121 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 0.0980 chunk 17 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 106 optimal weight: 0.0770 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.151849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.130417 restraints weight = 10107.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129952 restraints weight = 9949.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130365 restraints weight = 8874.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130546 restraints weight = 8015.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131010 restraints weight = 7241.969| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8019 Z= 0.085 Angle : 0.413 5.548 10999 Z= 0.223 Chirality : 0.041 0.261 1356 Planarity : 0.003 0.036 1453 Dihedral : 4.785 87.725 1321 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.70 % Favored : 95.13 % Rotamer: Outliers : 2.17 % Allowed : 30.12 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.25), residues: 1233 helix: 2.89 (0.20), residues: 660 sheet: -1.47 (0.37), residues: 197 loop : -1.18 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.015 0.001 TYR A 249 PHE 0.020 0.001 PHE B 25 TRP 0.006 0.001 TRP D 224 HIS 0.002 0.000 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00159 / 0.09 ( 8019) covalent geometry : angle 0.41254 / 0.22 (10999) hydrogen bonds : bond 0.02957 / 2.18 ( 584) hydrogen bonds : angle 3.69267 / 2.75 ( 1668) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.291 Fit side-chains REVERT: A 117 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7441 (pp) REVERT: A 151 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7920 (tttm) REVERT: A 185 ARG cc_start: 0.7677 (ttt-90) cc_final: 0.7467 (tmt170) outliers start: 11 outliers final: 9 residues processed: 117 average time/residue: 0.0775 time to fit residues: 12.9918 Evaluate side-chains 118 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 79 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.150510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128902 restraints weight = 10112.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.128305 restraints weight = 10592.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129823 restraints weight = 9045.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129843 restraints weight = 6942.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.130238 restraints weight = 6358.379| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8019 Z= 0.094 Angle : 0.423 5.505 10999 Z= 0.228 Chirality : 0.041 0.220 1356 Planarity : 0.003 0.037 1453 Dihedral : 4.952 88.041 1321 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.79 % Favored : 95.05 % Rotamer: Outliers : 2.17 % Allowed : 30.51 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.25), residues: 1233 helix: 2.83 (0.20), residues: 660 sheet: -1.40 (0.37), residues: 197 loop : -1.20 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.009 0.001 TYR A 371 PHE 0.018 0.001 PHE B 25 TRP 0.005 0.001 TRP D 224 HIS 0.002 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.09 ( 8019) covalent geometry : angle 0.42260 / 0.23 (10999) hydrogen bonds : bond 0.03098 / 2.28 ( 584) hydrogen bonds : angle 3.76212 / 2.79 ( 1668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1352.95 seconds wall clock time: 23 minutes 56.98 seconds (1436.98 seconds total)