Starting phenix.real_space_refine on Tue Aug 4 17:26:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y6n_72623/08_2026/9y6n_72623.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y6n_72623/08_2026/9y6n_72623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y6n_72623/08_2026/9y6n_72623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y6n_72623/08_2026/9y6n_72623.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y6n_72623/08_2026/9y6n_72623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y6n_72623/08_2026/9y6n_72623.map" } resolution = 2.68 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 3543 2.51 5 N 880 2.21 5 O 955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 5383 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1814 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 20, 'TRANS': 226} Chain breaks: 4 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1801 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 19, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 8, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1768 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 19, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 10, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 1.39, per 1000 atoms: 0.26 Number of scatterers: 5383 At special positions: 0 Unit cell: (88.298, 91.63, 60.809, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 955 8.00 N 880 7.00 C 3543 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: 0.36 Conformation dependent library (CDL) restraints added in 154.9 milliseconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 3.9% alpha, 63.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.508A pdb=" N ARG B 186 " --> pdb=" O GLN B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 87 removed outlier: 4.345A pdb=" N ALA A 118 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 117 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 138 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU B 277 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL B 282 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR B 267 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG B 264 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG B 254 " --> pdb=" O ARG B 264 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 266 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR B 288 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 211 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 87 removed outlier: 4.345A pdb=" N ALA A 118 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 117 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 138 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU B 277 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL B 282 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR B 267 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.547A pdb=" N VAL A 63 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA A 72 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 61 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 179 removed outlier: 4.019A pdb=" N ALA A 211 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TYR A 288 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE A 250 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR A 267 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA A 252 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 264 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 179 removed outlier: 4.019A pdb=" N ALA A 211 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TYR A 288 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE A 250 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR A 267 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA A 252 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR A 267 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL A 282 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 277 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 132 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA C 118 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 134 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N LEU C 116 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 42 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA C 118 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 87 removed outlier: 4.374A pdb=" N ALA B 118 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 153 " --> pdb=" O SER C 234 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU C 277 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL C 282 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR C 267 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ARG C 264 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG C 254 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY C 266 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TYR C 288 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA C 211 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 80 through 87 removed outlier: 4.374A pdb=" N ALA B 118 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 153 " --> pdb=" O SER C 234 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU C 277 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL C 282 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR C 267 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 192 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 264 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR C 194 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N GLY C 266 " --> pdb=" O THR C 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 74 removed outlier: 6.661A pdb=" N VAL B 63 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA B 72 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 61 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 68 through 74 removed outlier: 6.633A pdb=" N VAL C 63 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA C 72 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C 61 " --> pdb=" O ALA C 72 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 876 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: 0.72 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1651 1.34 - 1.46: 1087 1.46 - 1.57: 2783 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 5531 Sorted by residual: bond pdb=" N GLY C 229 " pdb=" CA GLY C 229 " ideal model delta sigma weight residual 1.443 1.486 -0.043 1.37e-02 5.33e+03 9.82e+00 bond pdb=" N ILE C 231 " pdb=" CA ILE C 231 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.27e-02 6.20e+03 7.96e+00 bond pdb=" N ILE B 231 " pdb=" CA ILE B 231 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.37e+00 bond pdb=" N ILE C 270 " pdb=" CA ILE C 270 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 6.82e+00 bond pdb=" N VAL B 237 " pdb=" CA VAL B 237 " ideal model delta sigma weight residual 1.468 1.496 -0.027 1.05e-02 9.07e+03 6.75e+00 ... (remaining 5526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 7225 1.26 - 2.51: 300 2.51 - 3.77: 73 3.77 - 5.03: 16 5.03 - 6.28: 8 Bond angle restraints: 7622 Sorted by residual: angle pdb=" CA THR A 219 " pdb=" CB THR A 219 " pdb=" OG1 THR A 219 " ideal model delta sigma weight residual 109.60 103.72 5.88 1.50e+00 4.44e-01 1.54e+01 angle pdb=" CA GLY C 229 " pdb=" C GLY C 229 " pdb=" N PRO C 230 " ideal model delta sigma weight residual 116.69 122.66 -5.97 1.71e+00 3.42e-01 1.22e+01 angle pdb=" CA GLY C 229 " pdb=" C GLY C 229 " pdb=" O GLY C 229 " ideal model delta sigma weight residual 121.52 116.76 4.76 1.43e+00 4.89e-01 1.11e+01 angle pdb=" CA GLU B 40 " pdb=" CB GLU B 40 " pdb=" CG GLU B 40 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 angle pdb=" CA THR A 223 " pdb=" CB THR A 223 " pdb=" OG1 THR A 223 " ideal model delta sigma weight residual 109.60 104.91 4.69 1.50e+00 4.44e-01 9.78e+00 ... (remaining 7617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 2855 17.78 - 35.57: 270 35.57 - 53.35: 55 53.35 - 71.13: 14 71.13 - 88.91: 2 Dihedral angle restraints: 3196 sinusoidal: 1090 harmonic: 2106 Sorted by residual: dihedral pdb=" CA ASP A 62 " pdb=" CB ASP A 62 " pdb=" CG ASP A 62 " pdb=" OD1 ASP A 62 " ideal model delta sinusoidal sigma weight residual -30.00 -84.10 54.10 1 2.00e+01 2.50e-03 9.93e+00 dihedral pdb=" CA ASP C 62 " pdb=" CB ASP C 62 " pdb=" CG ASP C 62 " pdb=" OD1 ASP C 62 " ideal model delta sinusoidal sigma weight residual -30.00 -83.15 53.15 1 2.00e+01 2.50e-03 9.61e+00 dihedral pdb=" N LEU A 244 " pdb=" CA LEU A 244 " pdb=" CB LEU A 244 " pdb=" CG LEU A 244 " ideal model delta sinusoidal sigma weight residual -60.00 -119.80 59.80 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 712 0.043 - 0.087: 133 0.087 - 0.130: 85 0.130 - 0.174: 0 0.174 - 0.217: 4 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA ILE C 270 " pdb=" N ILE C 270 " pdb=" C ILE C 270 " pdb=" CB ILE C 270 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE B 231 " pdb=" N ILE B 231 " pdb=" C ILE B 231 " pdb=" CB ILE B 231 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE C 231 " pdb=" N ILE C 231 " pdb=" C ILE C 231 " pdb=" CB ILE C 231 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 931 not shown) Planarity restraints: 937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 273 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" CD GLU B 273 " 0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU B 273 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 273 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 40 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" CD GLU B 40 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU B 40 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 40 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 40 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" CD GLU A 40 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A 40 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 40 " 0.011 2.00e-02 2.50e+03 ... (remaining 934 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 31 2.59 - 3.17: 4053 3.17 - 3.74: 7887 3.74 - 4.32: 11035 4.32 - 4.90: 19969 Nonbonded interactions: 42975 Sorted by model distance: nonbonded pdb=" OG1 THR C 168 " pdb=" OE1 GLN C 171 " model vdw 2.011 3.040 nonbonded pdb=" OH TYR A 123 " pdb=" O PRO B 129 " model vdw 2.059 3.040 nonbonded pdb=" OH TYR B 123 " pdb=" O PRO C 129 " model vdw 2.070 3.040 nonbonded pdb=" O PRO A 129 " pdb=" OH TYR C 123 " model vdw 2.076 3.040 nonbonded pdb=" O GLY B 65 " pdb=" OG1 THR B 68 " model vdw 2.222 3.040 ... (remaining 42970 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 38 or (resid 39 through 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 77 or (resid 78 and (name N or nam \ e CA or name C or name O or name CB )) or resid 79 through 163 or (resid 168 and \ (name N or name CA or name C or name O or name CB )) or resid 169 through 205 o \ r (resid 206 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 07 through 220 or (resid 221 and (name N or name CA or name C or name O or name \ CB )) or resid 222 through 238 or (resid 242 through 245 and (name N or name CA \ or name C or name O or name CB )) or resid 246 through 257 or (resid 258 and (na \ me N or name CA or name C or name O or name CB )) or resid 259 through 270 or (r \ esid 271 through 273 and (name N or name CA or name C or name O or name CB )) or \ resid 274 through 295)) selection = (chain 'B' and (resid 38 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 57 or (resid 58 through 59 and (na \ me N or name CA or name C or name O or name CB )) or resid 60 through 112 or (re \ sid 113 and (name N or name CA or name C or name O or name CB )) or resid 114 th \ rough 149 or (resid 150 through 151 and (name N or name CA or name C or name O o \ r name CB )) or resid 152 through 205 or (resid 206 and (name N or name CA or na \ me C or name O or name CB )) or resid 207 through 220 or (resid 221 and (name N \ or name CA or name C or name O or name CB )) or resid 222 through 223 or (resid \ 224 and (name N or name CA or name C or name O or name CB )) or resid 225 throug \ h 243 or (resid 244 through 245 and (name N or name CA or name C or name O or na \ me CB )) or resid 246 through 270 or (resid 271 through 273 and (name N or name \ CA or name C or name O or name CB )) or resid 274 through 292 or (resid 293 thro \ ugh 295 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 38 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 149 or (resid 150 through 151 a \ nd (name N or name CA or name C or name O or name CB )) or resid 152 through 163 \ or (resid 168 and (name N or name CA or name C or name O or name CB )) or resid \ 169 through 271 or (resid 272 through 273 and (name N or name CA or name C or n \ ame O or name CB )) or resid 274 through 292 or (resid 293 through 295 and (name \ N or name CA or name C or name O or name CB )))) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.680 Find NCS groups from input model: 0.070 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5531 Z= 0.276 Angle : 0.642 6.281 7622 Z= 0.348 Chirality : 0.045 0.217 934 Planarity : 0.005 0.036 937 Dihedral : 14.869 88.914 1834 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.92 % Allowed : 24.13 % Favored : 74.95 % 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: -0.61 (0.33), residues: 705 helix: -5.21 (0.16), residues: 18 sheet: -0.00 (0.26), residues: 416 loop : -0.52 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 110 TYR 0.016 0.002 TYR A 117 PHE 0.008 0.001 PHE A 156 TRP 0.008 0.001 TRP B 262 HIS 0.003 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.28 ( 5531) covalent geometry : angle 0.64227 / 0.35 ( 7622) hydrogen bonds : bond 0.15365 / 10.69 ( 246) hydrogen bonds : angle 6.53121 / 4.37 ( 876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7976 (tp30) cc_final: 0.7707 (tp30) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.7135 time to fit residues: 38.3357 Evaluate side-chains 40 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN B 265 ASN C 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.052772 restraints weight = 13197.214| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.96 r_work: 0.2660 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5531 Z= 0.180 Angle : 0.547 4.672 7622 Z= 0.270 Chirality : 0.043 0.137 934 Planarity : 0.004 0.028 937 Dihedral : 5.103 54.327 773 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.42 % Allowed : 21.73 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.51 (0.33), residues: 705 helix: -4.77 (0.36), residues: 18 sheet: -0.01 (0.27), residues: 413 loop : -0.33 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 110 TYR 0.012 0.001 TYR A 288 PHE 0.008 0.001 PHE C 156 TRP 0.008 0.001 TRP B 262 HIS 0.003 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 ( 5531) covalent geometry : angle 0.54738 / 0.27 ( 7622) hydrogen bonds : bond 0.03487 / 2.30 ( 246) hydrogen bonds : angle 4.84826 / 3.29 ( 876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8316 (tt) REVERT: B 195 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8822 (mp0) outliers start: 24 outliers final: 10 residues processed: 60 average time/residue: 0.5642 time to fit residues: 35.1253 Evaluate side-chains 49 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.051812 restraints weight = 13175.722| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.88 r_work: 0.2632 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 5531 Z= 0.288 Angle : 0.596 5.003 7622 Z= 0.291 Chirality : 0.045 0.138 934 Planarity : 0.005 0.031 937 Dihedral : 4.289 49.188 767 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.16 % Allowed : 22.47 % Favored : 72.38 % 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: -0.58 (0.32), residues: 705 helix: -4.42 (0.55), residues: 18 sheet: 0.00 (0.26), residues: 405 loop : -0.51 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 110 TYR 0.013 0.002 TYR A 288 PHE 0.009 0.002 PHE C 156 TRP 0.009 0.001 TRP A 262 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.29 ( 5531) covalent geometry : angle 0.59642 / 0.29 ( 7622) hydrogen bonds : bond 0.03638 / 2.39 ( 246) hydrogen bonds : angle 4.70631 / 3.19 ( 876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 39 time to evaluate : 0.128 Fit side-chains REVERT: A 244 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8283 (tt) REVERT: B 195 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8861 (mp0) outliers start: 28 outliers final: 12 residues processed: 66 average time/residue: 0.4979 time to fit residues: 34.1342 Evaluate side-chains 51 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.072040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.052302 restraints weight = 13155.504| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.95 r_work: 0.2649 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5531 Z= 0.187 Angle : 0.547 4.781 7622 Z= 0.269 Chirality : 0.043 0.134 934 Planarity : 0.004 0.031 937 Dihedral : 4.115 43.854 767 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.52 % Allowed : 21.92 % Favored : 72.56 % 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: -0.57 (0.32), residues: 705 helix: -4.27 (0.62), residues: 18 sheet: -0.01 (0.26), residues: 405 loop : -0.46 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.011 0.001 TYR A 288 PHE 0.008 0.001 PHE B 156 TRP 0.007 0.001 TRP A 262 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 5531) covalent geometry : angle 0.54736 / 0.27 ( 7622) hydrogen bonds : bond 0.03156 / 2.05 ( 246) hydrogen bonds : angle 4.50131 / 3.06 ( 876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 39 time to evaluate : 0.163 Fit side-chains REVERT: A 244 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8271 (tt) REVERT: B 195 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8808 (mp0) REVERT: B 264 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8249 (ttt-90) outliers start: 30 outliers final: 17 residues processed: 65 average time/residue: 0.4819 time to fit residues: 32.6106 Evaluate side-chains 57 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.071694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.051815 restraints weight = 13517.855| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.98 r_work: 0.2641 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5531 Z= 0.219 Angle : 0.565 5.031 7622 Z= 0.277 Chirality : 0.043 0.137 934 Planarity : 0.004 0.032 937 Dihedral : 4.051 36.389 767 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.71 % Allowed : 21.55 % Favored : 72.74 % 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: -0.57 (0.32), residues: 705 helix: -4.14 (0.67), residues: 18 sheet: 0.05 (0.26), residues: 399 loop : -0.59 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 264 TYR 0.011 0.002 TYR A 288 PHE 0.008 0.001 PHE C 156 TRP 0.007 0.001 TRP A 262 HIS 0.003 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 ( 5531) covalent geometry : angle 0.56481 / 0.28 ( 7622) hydrogen bonds : bond 0.03222 / 2.10 ( 246) hydrogen bonds : angle 4.46089 / 3.03 ( 876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 36 time to evaluate : 0.121 Fit side-chains REVERT: A 244 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8250 (tt) REVERT: B 195 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8882 (mp0) outliers start: 31 outliers final: 16 residues processed: 64 average time/residue: 0.4877 time to fit residues: 32.5045 Evaluate side-chains 53 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.052686 restraints weight = 13280.314| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.97 r_work: 0.2658 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5531 Z= 0.154 Angle : 0.537 5.580 7622 Z= 0.264 Chirality : 0.043 0.133 934 Planarity : 0.004 0.030 937 Dihedral : 3.880 30.962 767 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.05 % Allowed : 23.39 % Favored : 72.56 % 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: -0.54 (0.32), residues: 705 helix: -4.08 (0.67), residues: 18 sheet: 0.00 (0.26), residues: 404 loop : -0.45 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 264 TYR 0.009 0.001 TYR A 288 PHE 0.008 0.001 PHE B 156 TRP 0.006 0.001 TRP C 109 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.15 ( 5531) covalent geometry : angle 0.53704 / 0.26 ( 7622) hydrogen bonds : bond 0.02930 / 1.89 ( 246) hydrogen bonds : angle 4.29051 / 2.92 ( 876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 37 time to evaluate : 0.122 Fit side-chains REVERT: A 244 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8545 (tt) REVERT: B 195 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8802 (mp0) outliers start: 22 outliers final: 14 residues processed: 58 average time/residue: 0.4779 time to fit residues: 28.8463 Evaluate side-chains 51 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.073415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.054487 restraints weight = 13192.058| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.91 r_work: 0.2695 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5531 Z= 0.102 Angle : 0.521 6.368 7622 Z= 0.259 Chirality : 0.042 0.133 934 Planarity : 0.004 0.028 937 Dihedral : 3.604 25.037 767 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.31 % Allowed : 23.94 % Favored : 72.74 % 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: -0.42 (0.33), residues: 705 helix: -3.69 (0.77), residues: 18 sheet: 0.05 (0.26), residues: 404 loop : -0.35 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 264 TYR 0.007 0.001 TYR B 288 PHE 0.008 0.001 PHE B 156 TRP 0.008 0.001 TRP C 109 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.10 ( 5531) covalent geometry : angle 0.52134 / 0.26 ( 7622) hydrogen bonds : bond 0.02645 / 1.70 ( 246) hydrogen bonds : angle 4.07365 / 2.78 ( 876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.128 Fit side-chains REVERT: B 195 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8753 (mm-30) outliers start: 18 outliers final: 10 residues processed: 51 average time/residue: 0.5427 time to fit residues: 28.7172 Evaluate side-chains 46 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.053753 restraints weight = 13163.415| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.95 r_work: 0.2685 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5531 Z= 0.117 Angle : 0.524 6.637 7622 Z= 0.260 Chirality : 0.042 0.133 934 Planarity : 0.004 0.028 937 Dihedral : 3.568 22.622 767 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.76 % Allowed : 24.68 % Favored : 72.56 % 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: -0.39 (0.33), residues: 705 helix: -3.54 (0.83), residues: 18 sheet: 0.06 (0.27), residues: 404 loop : -0.32 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 264 TYR 0.008 0.001 TYR B 288 PHE 0.008 0.001 PHE A 156 TRP 0.009 0.001 TRP C 109 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 5531) covalent geometry : angle 0.52440 / 0.26 ( 7622) hydrogen bonds : bond 0.02665 / 1.72 ( 246) hydrogen bonds : angle 4.00976 / 2.73 ( 876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.124 Fit side-chains REVERT: A 52 GLU cc_start: 0.8229 (tt0) cc_final: 0.7756 (tt0) REVERT: B 195 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8805 (mm-30) outliers start: 15 outliers final: 10 residues processed: 50 average time/residue: 0.4973 time to fit residues: 25.8771 Evaluate side-chains 46 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 7 optimal weight: 0.0870 chunk 17 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.0030 chunk 38 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.053020 restraints weight = 13273.525| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.92 r_work: 0.2664 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5531 Z= 0.169 Angle : 0.561 7.271 7622 Z= 0.277 Chirality : 0.043 0.138 934 Planarity : 0.004 0.027 937 Dihedral : 3.688 22.293 767 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.13 % Allowed : 24.68 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.41 (0.33), residues: 705 helix: -3.54 (0.84), residues: 18 sheet: 0.11 (0.27), residues: 398 loop : -0.44 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 264 TYR 0.010 0.001 TYR B 288 PHE 0.009 0.001 PHE A 156 TRP 0.007 0.001 TRP A 262 HIS 0.002 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 ( 5531) covalent geometry : angle 0.56065 / 0.28 ( 7622) hydrogen bonds : bond 0.02863 / 1.86 ( 246) hydrogen bonds : angle 4.10315 / 2.79 ( 876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.169 Fit side-chains REVERT: A 155 GLN cc_start: 0.8371 (tt0) cc_final: 0.7864 (mt0) REVERT: B 195 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8787 (mm-30) REVERT: B 264 ARG cc_start: 0.8507 (ttt-90) cc_final: 0.8152 (ttt-90) outliers start: 17 outliers final: 12 residues processed: 52 average time/residue: 0.5657 time to fit residues: 30.6121 Evaluate side-chains 50 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.052577 restraints weight = 13266.500| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.95 r_work: 0.2652 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5531 Z= 0.183 Angle : 0.566 6.906 7622 Z= 0.279 Chirality : 0.043 0.137 934 Planarity : 0.004 0.027 937 Dihedral : 3.772 21.918 767 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.95 % Allowed : 24.86 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.45 (0.33), residues: 705 helix: -3.49 (0.83), residues: 18 sheet: 0.08 (0.27), residues: 398 loop : -0.46 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 264 TYR 0.010 0.001 TYR B 288 PHE 0.008 0.001 PHE B 156 TRP 0.007 0.001 TRP A 262 HIS 0.002 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.18 ( 5531) covalent geometry : angle 0.56587 / 0.28 ( 7622) hydrogen bonds : bond 0.02916 / 1.89 ( 246) hydrogen bonds : angle 4.15397 / 2.82 ( 876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.203 Fit side-chains REVERT: A 52 GLU cc_start: 0.8230 (tt0) cc_final: 0.7819 (tt0) REVERT: A 155 GLN cc_start: 0.8396 (tt0) cc_final: 0.7824 (mt0) REVERT: B 195 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8778 (mm-30) outliers start: 16 outliers final: 13 residues processed: 54 average time/residue: 0.5698 time to fit residues: 31.9778 Evaluate side-chains 51 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.052639 restraints weight = 13145.129| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.95 r_work: 0.2662 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5531 Z= 0.173 Angle : 0.570 7.274 7622 Z= 0.282 Chirality : 0.043 0.137 934 Planarity : 0.004 0.027 937 Dihedral : 3.778 21.794 767 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.31 % Allowed : 24.49 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.46 (0.33), residues: 705 helix: -3.43 (0.86), residues: 18 sheet: 0.02 (0.27), residues: 404 loop : -0.38 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 264 TYR 0.010 0.001 TYR B 288 PHE 0.008 0.001 PHE A 156 TRP 0.007 0.001 TRP A 262 HIS 0.002 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.17 ( 5531) covalent geometry : angle 0.57039 / 0.28 ( 7622) hydrogen bonds : bond 0.02878 / 1.87 ( 246) hydrogen bonds : angle 4.13448 / 2.81 ( 876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1310.03 seconds wall clock time: 23 minutes 0.19 seconds (1380.19 seconds total)