Starting phenix.real_space_refine on Tue Mar 3 20:03:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e9y_27968/03_2026/8e9y_27968.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9y_27968/03_2026/8e9y_27968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e9y_27968/03_2026/8e9y_27968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9y_27968/03_2026/8e9y_27968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e9y_27968/03_2026/8e9y_27968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9y_27968/03_2026/8e9y_27968.map" } resolution = 2.79 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= 0.021 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 56 5.16 5 Cl 1 4.86 5 C 5423 2.51 5 N 1437 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8479 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2173 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1658 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 6, 'ASP:plan': 6, 'ASN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2498 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 385 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1741 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WE9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.22 Number of scatterers: 8479 At special positions: 0 Unit cell: (88, 118.8, 124.96, 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) Cl 1 17.00 S 56 16.00 O 1562 8.00 N 1437 7.00 C 5423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 331.9 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 37.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 67 through 96 removed outlier: 3.750A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 103 through 120 removed outlier: 4.027A pdb=" N LEU A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 139 through 172 removed outlier: 4.122A pdb=" N TRP A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 145 " --> pdb=" O CYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.529A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 206 removed outlier: 3.747A pdb=" N SER A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Proline residue: A 202 - end of helix removed outlier: 3.615A pdb=" N PHE A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.914A pdb=" N PHE A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.504A pdb=" N LEU A 226 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 227 " --> pdb=" O GLN A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 240 through 265 removed outlier: 3.544A pdb=" N TYR A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 502 removed outlier: 3.879A pdb=" N ALA A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 Processing helix chain 'A' and resid 522 through 533 Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.743A pdb=" N THR A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.565A pdb=" N THR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 30 Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.359A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 removed outlier: 3.662A pdb=" N ILE B 97 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP B 102 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.674A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 185 through 196 removed outlier: 4.155A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 244 removed outlier: 4.098A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.521A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.888A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 9 through 25 removed outlier: 4.018A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.558A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.827A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 76 removed outlier: 9.935A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.395A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.628A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 81 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.361A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.584A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.817A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.942A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.439A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.738A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.076A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.076A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 4.151A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 147 401 hydrogen bonds defined for protein. 1122 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: 1.33 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2169 1.33 - 1.45: 1827 1.45 - 1.58: 4589 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8664 Sorted by residual: bond pdb=" C15 WE9 A 801 " pdb=" N24 WE9 A 801 " ideal model delta sigma weight residual 1.289 1.445 -0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C15 WE9 A 801 " pdb=" N16 WE9 A 801 " ideal model delta sigma weight residual 1.356 1.461 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" N19 WE9 A 801 " pdb=" O21 WE9 A 801 " ideal model delta sigma weight residual 1.352 1.454 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C22 WE9 A 801 " pdb=" N19 WE9 A 801 " ideal model delta sigma weight residual 1.511 1.416 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C06 WE9 A 801 " pdb=" N24 WE9 A 801 " ideal model delta sigma weight residual 1.378 1.466 -0.088 2.00e-02 2.50e+03 1.91e+01 ... (remaining 8659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 11470 2.07 - 4.14: 259 4.14 - 6.21: 61 6.21 - 8.27: 16 8.27 - 10.34: 3 Bond angle restraints: 11809 Sorted by residual: angle pdb=" N TYR B 191 " pdb=" CA TYR B 191 " pdb=" C TYR B 191 " ideal model delta sigma weight residual 113.38 104.98 8.40 1.23e+00 6.61e-01 4.67e+01 angle pdb=" N ILE B 193 " pdb=" CA ILE B 193 " pdb=" C ILE B 193 " ideal model delta sigma weight residual 110.42 103.98 6.44 9.60e-01 1.09e+00 4.50e+01 angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " ideal model delta sigma weight residual 117.38 124.90 -7.52 1.18e+00 7.18e-01 4.06e+01 angle pdb=" N ILE B 200 " pdb=" CA ILE B 200 " pdb=" C ILE B 200 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.92e+01 angle pdb=" N VAL B 198 " pdb=" CA VAL B 198 " pdb=" C VAL B 198 " ideal model delta sigma weight residual 113.20 107.44 5.76 9.60e-01 1.09e+00 3.60e+01 ... (remaining 11804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 4523 15.00 - 29.99: 420 29.99 - 44.99: 108 44.99 - 59.99: 15 59.99 - 74.98: 9 Dihedral angle restraints: 5075 sinusoidal: 1815 harmonic: 3260 Sorted by residual: dihedral pdb=" CA ASN D 24 " pdb=" C ASN D 24 " pdb=" N ILE D 25 " pdb=" CA ILE D 25 " ideal model delta harmonic sigma weight residual -180.00 -157.06 -22.94 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TYR E 161 " pdb=" C TYR E 161 " pdb=" N LEU E 162 " pdb=" CA LEU E 162 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 5072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1090 0.054 - 0.108: 242 0.108 - 0.162: 35 0.162 - 0.215: 4 0.215 - 0.269: 5 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CA ILE B 193 " pdb=" N ILE B 193 " pdb=" C ILE B 193 " pdb=" CB ILE B 193 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA GLU B 182 " pdb=" N GLU B 182 " pdb=" C GLU B 182 " pdb=" CB GLU B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE B 200 " pdb=" N ILE B 200 " pdb=" C ILE B 200 " pdb=" CB ILE B 200 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1373 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 212 " 0.063 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO B 213 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 193 " -0.018 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE B 193 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE B 193 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG B 194 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 222 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C GLU E 222 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU E 222 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR E 223 " -0.019 2.00e-02 2.50e+03 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1185 2.75 - 3.29: 8449 3.29 - 3.83: 14129 3.83 - 4.36: 16990 4.36 - 4.90: 29102 Nonbonded interactions: 69855 Sorted by model distance: nonbonded pdb=" O SER B 44 " pdb=" ND2 ASN B 144 " model vdw 2.217 3.120 nonbonded pdb=" OG1 THR A 82 " pdb=" OG1 THR A 538 " model vdw 2.220 3.040 nonbonded pdb=" NH2 ARG A 177 " pdb=" OH TYR B 243 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR C 264 " pdb=" O ALA C 299 " model vdw 2.243 3.040 nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.244 3.040 ... (remaining 69850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.200 Find NCS groups from input model: 0.040 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:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 0.156 8667 Z= 0.303 Angle : 0.784 10.342 11815 Z= 0.488 Chirality : 0.048 0.269 1376 Planarity : 0.004 0.096 1490 Dihedral : 13.125 74.984 2960 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.12 % Allowed : 1.16 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.06 (0.25), residues: 1105 helix: -0.41 (0.26), residues: 374 sheet: -0.27 (0.32), residues: 259 loop : -1.06 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 32 TYR 0.017 0.002 TYR B 170 PHE 0.024 0.002 PHE B 84 TRP 0.010 0.001 TRP A 504 HIS 0.014 0.002 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 8664) covalent geometry : angle 0.78387 (11809) SS BOND : bond 0.00412 ( 3) SS BOND : angle 0.66029 ( 6) hydrogen bonds : bond 0.23250 ( 397) hydrogen bonds : angle 7.98643 ( 1122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.294 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 172 average time/residue: 0.3943 time to fit residues: 73.7371 Evaluate side-chains 161 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** E 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.160854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.140855 restraints weight = 11942.606| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.81 r_work: 0.3734 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8667 Z= 0.157 Angle : 0.627 8.243 11815 Z= 0.331 Chirality : 0.044 0.171 1376 Planarity : 0.004 0.072 1490 Dihedral : 4.744 23.574 1222 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.08 % Allowed : 10.52 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1105 helix: 0.28 (0.26), residues: 390 sheet: -0.28 (0.31), residues: 271 loop : -0.83 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 15 TYR 0.020 0.002 TYR B 170 PHE 0.016 0.002 PHE B 84 TRP 0.012 0.001 TRP A 526 HIS 0.013 0.002 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8664) covalent geometry : angle 0.62728 (11809) SS BOND : bond 0.00541 ( 3) SS BOND : angle 0.74274 ( 6) hydrogen bonds : bond 0.04836 ( 397) hydrogen bonds : angle 5.39307 ( 1122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.321 Fit side-chains REVERT: B 35 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7222 (mtm-85) REVERT: B 244 ASN cc_start: 0.8350 (m110) cc_final: 0.8046 (m110) REVERT: C 251 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7308 (mtt90) REVERT: E 95 TYR cc_start: 0.8445 (m-80) cc_final: 0.7973 (m-80) outliers start: 18 outliers final: 9 residues processed: 174 average time/residue: 0.4561 time to fit residues: 85.3053 Evaluate side-chains 175 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 0.0060 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 56 optimal weight: 0.0980 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN B 131 ASN C 17 GLN C 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.162554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142733 restraints weight = 11781.544| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.81 r_work: 0.3760 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8667 Z= 0.112 Angle : 0.547 6.740 11815 Z= 0.289 Chirality : 0.042 0.140 1376 Planarity : 0.004 0.059 1490 Dihedral : 4.434 21.731 1221 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 2.31 % Allowed : 13.41 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.29 (0.26), residues: 1105 helix: 0.61 (0.27), residues: 400 sheet: -0.09 (0.31), residues: 269 loop : -0.90 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 194 TYR 0.018 0.002 TYR A 176 PHE 0.017 0.001 PHE B 84 TRP 0.008 0.001 TRP A 526 HIS 0.010 0.002 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8664) covalent geometry : angle 0.54751 (11809) SS BOND : bond 0.00307 ( 3) SS BOND : angle 0.49452 ( 6) hydrogen bonds : bond 0.03981 ( 397) hydrogen bonds : angle 4.90248 ( 1122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.302 Fit side-chains REVERT: B 35 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7162 (mtm-85) REVERT: B 242 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6999 (mm-30) REVERT: B 244 ASN cc_start: 0.8333 (m110) cc_final: 0.8035 (m110) REVERT: C 251 ARG cc_start: 0.7525 (mtt180) cc_final: 0.7292 (mtt90) REVERT: E 79 LEU cc_start: 0.7591 (pt) cc_final: 0.7208 (pt) REVERT: E 95 TYR cc_start: 0.8404 (m-80) cc_final: 0.8046 (m-80) outliers start: 20 outliers final: 4 residues processed: 178 average time/residue: 0.4338 time to fit residues: 83.3597 Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 73 optimal weight: 0.0570 chunk 81 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.160617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.140848 restraints weight = 11955.843| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.75 r_work: 0.3737 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8667 Z= 0.156 Angle : 0.580 7.515 11815 Z= 0.303 Chirality : 0.043 0.149 1376 Planarity : 0.004 0.052 1490 Dihedral : 4.544 22.193 1221 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.89 % Favored : 95.02 % Rotamer: Outliers : 2.20 % Allowed : 15.61 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.21 (0.26), residues: 1105 helix: 0.74 (0.27), residues: 397 sheet: -0.01 (0.31), residues: 269 loop : -0.95 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 169 TYR 0.015 0.002 TYR A 176 PHE 0.016 0.002 PHE B 84 TRP 0.007 0.001 TRP C 169 HIS 0.010 0.002 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8664) covalent geometry : angle 0.58001 (11809) SS BOND : bond 0.00413 ( 3) SS BOND : angle 0.59318 ( 6) hydrogen bonds : bond 0.03958 ( 397) hydrogen bonds : angle 4.80921 ( 1122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.298 Fit side-chains REVERT: A 544 TYR cc_start: 0.7846 (m-80) cc_final: 0.7534 (m-80) REVERT: B 35 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7225 (mtm-85) REVERT: B 242 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7093 (mm-30) REVERT: B 244 ASN cc_start: 0.8298 (m110) cc_final: 0.7954 (m110) REVERT: C 251 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7307 (mtt90) REVERT: C 314 ARG cc_start: 0.7188 (ptm-80) cc_final: 0.6985 (ptt180) REVERT: E 95 TYR cc_start: 0.8424 (m-80) cc_final: 0.8060 (m-80) outliers start: 19 outliers final: 10 residues processed: 171 average time/residue: 0.4401 time to fit residues: 81.2366 Evaluate side-chains 165 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN C 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.160686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.140899 restraints weight = 11929.623| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.74 r_work: 0.3739 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8667 Z= 0.144 Angle : 0.577 7.286 11815 Z= 0.299 Chirality : 0.042 0.140 1376 Planarity : 0.004 0.047 1490 Dihedral : 4.518 21.901 1221 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 2.43 % Allowed : 18.27 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.14 (0.26), residues: 1105 helix: 0.93 (0.27), residues: 388 sheet: 0.00 (0.31), residues: 269 loop : -0.99 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 169 TYR 0.029 0.002 TYR A 176 PHE 0.017 0.002 PHE B 84 TRP 0.007 0.001 TRP C 169 HIS 0.009 0.002 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8664) covalent geometry : angle 0.57742 (11809) SS BOND : bond 0.00353 ( 3) SS BOND : angle 0.58214 ( 6) hydrogen bonds : bond 0.03783 ( 397) hydrogen bonds : angle 4.72856 ( 1122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.303 Fit side-chains REVERT: A 544 TYR cc_start: 0.7872 (m-80) cc_final: 0.7516 (m-80) REVERT: B 35 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7194 (mtm-85) REVERT: B 242 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7086 (mm-30) REVERT: B 244 ASN cc_start: 0.8292 (m110) cc_final: 0.7961 (m110) REVERT: C 219 ARG cc_start: 0.6934 (mmm160) cc_final: 0.6708 (mtt180) REVERT: C 314 ARG cc_start: 0.7188 (ptm-80) cc_final: 0.6983 (ptt180) REVERT: E 95 TYR cc_start: 0.8432 (m-80) cc_final: 0.8045 (m-80) outliers start: 21 outliers final: 10 residues processed: 169 average time/residue: 0.4622 time to fit residues: 83.8110 Evaluate side-chains 163 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.159988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140011 restraints weight = 11763.349| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.80 r_work: 0.3723 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8667 Z= 0.168 Angle : 0.593 7.387 11815 Z= 0.307 Chirality : 0.043 0.167 1376 Planarity : 0.004 0.044 1490 Dihedral : 4.575 21.891 1221 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 2.77 % Allowed : 18.73 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.18 (0.26), residues: 1105 helix: 0.90 (0.27), residues: 387 sheet: -0.02 (0.31), residues: 269 loop : -1.01 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 169 TYR 0.024 0.002 TYR A 176 PHE 0.027 0.002 PHE A 222 TRP 0.008 0.001 TRP C 211 HIS 0.009 0.002 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8664) covalent geometry : angle 0.59256 (11809) SS BOND : bond 0.00413 ( 3) SS BOND : angle 0.71697 ( 6) hydrogen bonds : bond 0.03856 ( 397) hydrogen bonds : angle 4.72401 ( 1122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.329 Fit side-chains REVERT: A 246 ILE cc_start: 0.7952 (mp) cc_final: 0.7661 (mt) REVERT: A 544 TYR cc_start: 0.7880 (m-80) cc_final: 0.7516 (m-80) REVERT: B 35 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7209 (mtm-85) REVERT: B 242 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7084 (mm-30) REVERT: B 244 ASN cc_start: 0.8304 (m110) cc_final: 0.7967 (m110) REVERT: E 95 TYR cc_start: 0.8457 (m-80) cc_final: 0.8088 (m-80) outliers start: 24 outliers final: 13 residues processed: 171 average time/residue: 0.4370 time to fit residues: 80.7948 Evaluate side-chains 172 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 93 optimal weight: 0.0050 chunk 35 optimal weight: 0.0870 chunk 36 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 41 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 overall best weight: 0.1570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.162899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.142917 restraints weight = 12085.457| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.84 r_work: 0.3760 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8667 Z= 0.106 Angle : 0.554 7.664 11815 Z= 0.286 Chirality : 0.042 0.133 1376 Planarity : 0.004 0.041 1490 Dihedral : 4.344 19.560 1221 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.07 % Favored : 95.84 % Rotamer: Outliers : 2.08 % Allowed : 20.23 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.04 (0.26), residues: 1105 helix: 1.00 (0.28), residues: 387 sheet: -0.02 (0.31), residues: 277 loop : -0.87 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 169 TYR 0.018 0.001 TYR A 176 PHE 0.017 0.001 PHE C 335 TRP 0.010 0.001 TRP C 169 HIS 0.007 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8664) covalent geometry : angle 0.55405 (11809) SS BOND : bond 0.00334 ( 3) SS BOND : angle 0.65359 ( 6) hydrogen bonds : bond 0.03320 ( 397) hydrogen bonds : angle 4.58587 ( 1122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.255 Fit side-chains REVERT: A 246 ILE cc_start: 0.7847 (mp) cc_final: 0.7581 (mt) REVERT: B 35 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7108 (mtm-85) REVERT: B 242 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7188 (mm-30) REVERT: B 244 ASN cc_start: 0.8270 (m110) cc_final: 0.7944 (m-40) REVERT: C 234 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: E 95 TYR cc_start: 0.8404 (m-80) cc_final: 0.8061 (m-80) outliers start: 18 outliers final: 9 residues processed: 172 average time/residue: 0.4328 time to fit residues: 80.3832 Evaluate side-chains 166 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.160403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.140649 restraints weight = 11887.092| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.75 r_work: 0.3738 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8667 Z= 0.156 Angle : 0.590 7.639 11815 Z= 0.305 Chirality : 0.043 0.173 1376 Planarity : 0.004 0.044 1490 Dihedral : 4.481 20.147 1221 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 2.20 % Allowed : 21.16 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.11 (0.26), residues: 1105 helix: 0.93 (0.27), residues: 388 sheet: -0.06 (0.30), residues: 279 loop : -0.90 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 169 TYR 0.020 0.002 TYR A 534 PHE 0.018 0.002 PHE B 84 TRP 0.009 0.001 TRP A 144 HIS 0.008 0.002 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8664) covalent geometry : angle 0.58988 (11809) SS BOND : bond 0.00329 ( 3) SS BOND : angle 0.47384 ( 6) hydrogen bonds : bond 0.03683 ( 397) hydrogen bonds : angle 4.64646 ( 1122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.235 Fit side-chains REVERT: A 246 ILE cc_start: 0.7902 (mp) cc_final: 0.7619 (mt) REVERT: B 35 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7232 (mtm-85) REVERT: B 242 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7162 (mm-30) REVERT: B 244 ASN cc_start: 0.8243 (m110) cc_final: 0.7940 (m-40) REVERT: C 255 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7140 (mp) REVERT: E 95 TYR cc_start: 0.8427 (m-80) cc_final: 0.8050 (m-80) outliers start: 19 outliers final: 10 residues processed: 170 average time/residue: 0.4576 time to fit residues: 83.7365 Evaluate side-chains 170 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 75 optimal weight: 0.2980 chunk 7 optimal weight: 0.0070 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 overall best weight: 0.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN C 17 GLN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.162036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142125 restraints weight = 11942.438| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.82 r_work: 0.3757 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8667 Z= 0.112 Angle : 0.567 7.061 11815 Z= 0.291 Chirality : 0.042 0.165 1376 Planarity : 0.004 0.043 1490 Dihedral : 4.389 18.775 1221 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 2.20 % Allowed : 21.73 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.05 (0.26), residues: 1105 helix: 1.01 (0.27), residues: 388 sheet: -0.04 (0.30), residues: 277 loop : -0.88 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.018 0.002 TYR A 534 PHE 0.032 0.001 PHE A 222 TRP 0.008 0.001 TRP C 169 HIS 0.007 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8664) covalent geometry : angle 0.56713 (11809) SS BOND : bond 0.00283 ( 3) SS BOND : angle 0.35918 ( 6) hydrogen bonds : bond 0.03396 ( 397) hydrogen bonds : angle 4.58908 ( 1122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.300 Fit side-chains REVERT: A 246 ILE cc_start: 0.7884 (mp) cc_final: 0.7598 (mt) REVERT: B 35 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7160 (mtm-85) REVERT: B 242 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7022 (mm-30) REVERT: B 244 ASN cc_start: 0.8252 (m110) cc_final: 0.7909 (m-40) REVERT: C 255 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7108 (mp) REVERT: E 95 TYR cc_start: 0.8396 (m-80) cc_final: 0.8087 (m-80) outliers start: 19 outliers final: 12 residues processed: 164 average time/residue: 0.4596 time to fit residues: 81.0966 Evaluate side-chains 170 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 71 optimal weight: 0.0470 chunk 68 optimal weight: 0.0570 chunk 53 optimal weight: 0.2980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.162009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142083 restraints weight = 11858.742| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.81 r_work: 0.3753 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 8667 Z= 0.170 Angle : 0.897 59.200 11815 Z= 0.514 Chirality : 0.043 0.232 1376 Planarity : 0.004 0.074 1490 Dihedral : 4.414 18.765 1221 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 1.62 % Allowed : 22.43 % Favored : 75.95 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.94 % 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: -0.05 (0.26), residues: 1105 helix: 0.99 (0.27), residues: 388 sheet: -0.04 (0.30), residues: 277 loop : -0.87 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 184 TYR 0.018 0.002 TYR A 534 PHE 0.019 0.001 PHE C 335 TRP 0.008 0.001 TRP C 169 HIS 0.007 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8664) covalent geometry : angle 0.89702 (11809) SS BOND : bond 0.00253 ( 3) SS BOND : angle 0.32459 ( 6) hydrogen bonds : bond 0.03400 ( 397) hydrogen bonds : angle 4.59750 ( 1122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.237 Fit side-chains REVERT: A 246 ILE cc_start: 0.7885 (mp) cc_final: 0.7600 (mt) REVERT: B 35 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7171 (mtm-85) REVERT: B 242 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6999 (mm-30) REVERT: C 150 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.8070 (mpt180) REVERT: C 255 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7113 (mp) REVERT: E 95 TYR cc_start: 0.8396 (m-80) cc_final: 0.8092 (m-80) outliers start: 14 outliers final: 12 residues processed: 158 average time/residue: 0.4649 time to fit residues: 79.0062 Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 0.0000 chunk 37 optimal weight: 0.7980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.162046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142142 restraints weight = 11847.142| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.81 r_work: 0.3751 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 8667 Z= 0.170 Angle : 0.897 59.195 11815 Z= 0.514 Chirality : 0.043 0.232 1376 Planarity : 0.004 0.074 1490 Dihedral : 4.414 18.765 1221 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 1.62 % Allowed : 22.31 % Favored : 76.07 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.94 % 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: -0.05 (0.26), residues: 1105 helix: 0.99 (0.27), residues: 388 sheet: -0.04 (0.30), residues: 277 loop : -0.87 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 184 TYR 0.018 0.002 TYR A 534 PHE 0.019 0.001 PHE C 335 TRP 0.008 0.001 TRP C 169 HIS 0.007 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8664) covalent geometry : angle 0.89698 (11809) SS BOND : bond 0.00253 ( 3) SS BOND : angle 0.32459 ( 6) hydrogen bonds : bond 0.03400 ( 397) hydrogen bonds : angle 4.59750 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3285.23 seconds wall clock time: 56 minutes 31.25 seconds (3391.25 seconds total)