Starting phenix.real_space_refine on Sat Jul 26 08:38:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e9y_27968/07_2025/8e9y_27968.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9y_27968/07_2025/8e9y_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e9y_27968/07_2025/8e9y_27968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9y_27968/07_2025/8e9y_27968.map" model { file = "/net/cci-nas-00/data/ceres_data/8e9y_27968/07_2025/8e9y_27968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9y_27968/07_2025/8e9y_27968.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP: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: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 6, 'ASP: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, 'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 1, 'GLU:plan': 7, '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: 5.68, per 1000 atoms: 0.67 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: 2.28 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.17 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: 2.65 Time building geometry restraints manager: 2.63 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.760 ------------------------------------------------------------------------------- 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 : 12.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (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 TRP 0.010 0.001 TRP A 504 HIS 0.014 0.002 HIS B 82 PHE 0.024 0.002 PHE B 84 TYR 0.017 0.002 TYR B 170 ARG 0.006 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.23250 ( 397) hydrogen bonds : angle 7.98643 ( 1122) SS BOND : bond 0.00412 ( 3) SS BOND : angle 0.66029 ( 6) covalent geometry : bond 0.00555 ( 8664) covalent geometry : angle 0.78387 (11809) *********************** 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 : 0.981 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 172 average time/residue: 0.8257 time to fit residues: 155.1823 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 : 0.951 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.0000 chunk 33 optimal weight: 0.0970 chunk 51 optimal weight: 0.0170 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 overall best weight: 0.2620 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.162562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.142669 restraints weight = 11765.982| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.80 r_work: 0.3763 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8667 Z= 0.130 Angle : 0.612 8.033 11815 Z= 0.320 Chirality : 0.043 0.161 1376 Planarity : 0.004 0.069 1490 Dihedral : 4.650 22.784 1222 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.85 % Allowed : 10.52 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1105 helix: 0.31 (0.26), residues: 394 sheet: -0.28 (0.31), residues: 271 loop : -0.82 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 526 HIS 0.011 0.002 HIS B 82 PHE 0.016 0.001 PHE B 84 TYR 0.018 0.002 TYR B 170 ARG 0.005 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 397) hydrogen bonds : angle 5.34527 ( 1122) SS BOND : bond 0.00517 ( 3) SS BOND : angle 0.70388 ( 6) covalent geometry : bond 0.00268 ( 8664) covalent geometry : angle 0.61182 (11809) *********************** 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: 16 poor density : 172 time to evaluate : 0.872 Fit side-chains REVERT: B 35 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7180 (mtm-85) REVERT: C 150 ARG cc_start: 0.8537 (mmt-90) cc_final: 0.8315 (mmt180) REVERT: C 251 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7347 (mtt90) REVERT: C 335 PHE cc_start: 0.7984 (m-80) cc_final: 0.7624 (m-80) REVERT: E 95 TYR cc_start: 0.8413 (m-80) cc_final: 0.8005 (m-80) outliers start: 16 outliers final: 6 residues processed: 176 average time/residue: 0.9519 time to fit residues: 181.1373 Evaluate side-chains 174 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 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 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN B 131 ASN C 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.160145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.140165 restraints weight = 11898.175| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.82 r_work: 0.3726 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8667 Z= 0.161 Angle : 0.591 7.394 11815 Z= 0.310 Chirality : 0.043 0.156 1376 Planarity : 0.004 0.061 1490 Dihedral : 4.602 23.207 1221 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 1.85 % Allowed : 13.41 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1105 helix: 0.57 (0.27), residues: 396 sheet: -0.17 (0.31), residues: 271 loop : -0.95 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 144 HIS 0.012 0.002 HIS B 82 PHE 0.018 0.002 PHE B 84 TYR 0.025 0.002 TYR A 176 ARG 0.005 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 397) hydrogen bonds : angle 5.03985 ( 1122) SS BOND : bond 0.00456 ( 3) SS BOND : angle 0.56359 ( 6) covalent geometry : bond 0.00362 ( 8664) covalent geometry : angle 0.59058 (11809) *********************** 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 178 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.869 Fit side-chains REVERT: A 544 TYR cc_start: 0.7802 (m-80) cc_final: 0.7409 (m-80) REVERT: B 35 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7234 (mtm-85) REVERT: B 244 ASN cc_start: 0.8323 (m110) cc_final: 0.8042 (m110) REVERT: E 95 TYR cc_start: 0.8453 (m-80) cc_final: 0.8064 (m-80) outliers start: 16 outliers final: 5 residues processed: 171 average time/residue: 0.9549 time to fit residues: 176.3229 Evaluate side-chains 160 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 C residue 340 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 5 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 46 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.159972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.139838 restraints weight = 11797.136| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.81 r_work: 0.3722 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8667 Z= 0.164 Angle : 0.593 7.663 11815 Z= 0.309 Chirality : 0.043 0.157 1376 Planarity : 0.004 0.053 1490 Dihedral : 4.634 23.213 1221 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 1.85 % Allowed : 16.65 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1105 helix: 0.66 (0.27), residues: 396 sheet: -0.18 (0.31), residues: 266 loop : -0.98 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 211 HIS 0.010 0.002 HIS B 82 PHE 0.016 0.002 PHE B 84 TYR 0.026 0.002 TYR A 176 ARG 0.010 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 397) hydrogen bonds : angle 4.92733 ( 1122) SS BOND : bond 0.00434 ( 3) SS BOND : angle 0.61018 ( 6) covalent geometry : bond 0.00373 ( 8664) covalent geometry : angle 0.59323 (11809) *********************** 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 173 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.888 Fit side-chains REVERT: A 544 TYR cc_start: 0.7825 (m-80) cc_final: 0.7434 (m-80) REVERT: B 35 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7237 (mtm-85) REVERT: B 242 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 244 ASN cc_start: 0.8312 (m110) cc_final: 0.8015 (m110) REVERT: E 95 TYR cc_start: 0.8465 (m-80) cc_final: 0.8048 (m-80) outliers start: 16 outliers final: 8 residues processed: 165 average time/residue: 0.9326 time to fit residues: 166.3768 Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 122 LEU 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 70 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN ** E 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.159486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139377 restraints weight = 11807.116| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.81 r_work: 0.3717 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8667 Z= 0.176 Angle : 0.604 7.465 11815 Z= 0.314 Chirality : 0.044 0.179 1376 Planarity : 0.004 0.049 1490 Dihedral : 4.696 23.015 1221 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1105 helix: 0.79 (0.27), residues: 388 sheet: -0.15 (0.31), residues: 266 loop : -1.03 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 133 HIS 0.010 0.002 HIS B 82 PHE 0.019 0.002 PHE B 81 TYR 0.028 0.002 TYR A 176 ARG 0.007 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 397) hydrogen bonds : angle 4.85411 ( 1122) SS BOND : bond 0.00393 ( 3) SS BOND : angle 0.61181 ( 6) covalent geometry : bond 0.00403 ( 8664) covalent geometry : angle 0.60350 (11809) *********************** 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 181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.883 Fit side-chains REVERT: A 544 TYR cc_start: 0.7854 (m-80) cc_final: 0.7474 (m-80) REVERT: B 35 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7230 (mtm-85) REVERT: B 242 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7102 (mm-30) REVERT: C 68 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7724 (ttt-90) REVERT: C 219 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6623 (mtm180) REVERT: E 95 TYR cc_start: 0.8471 (m-80) cc_final: 0.8023 (m-80) outliers start: 21 outliers final: 12 residues processed: 170 average time/residue: 1.0992 time to fit residues: 200.7941 Evaluate side-chains 172 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 236 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 340 ASN 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 10 optimal weight: 0.0670 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 15 optimal weight: 0.0020 chunk 64 optimal weight: 0.0170 chunk 97 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.161434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141731 restraints weight = 11807.877| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.73 r_work: 0.3751 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8667 Z= 0.115 Angle : 0.563 6.563 11815 Z= 0.291 Chirality : 0.042 0.142 1376 Planarity : 0.004 0.043 1490 Dihedral : 4.519 21.321 1221 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 3.12 % Allowed : 18.96 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1105 helix: 0.97 (0.28), residues: 387 sheet: -0.09 (0.31), residues: 264 loop : -0.98 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.009 0.001 HIS B 82 PHE 0.024 0.001 PHE A 222 TYR 0.020 0.001 TYR A 176 ARG 0.005 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 397) hydrogen bonds : angle 4.71697 ( 1122) SS BOND : bond 0.00294 ( 3) SS BOND : angle 0.53925 ( 6) covalent geometry : bond 0.00249 ( 8664) covalent geometry : angle 0.56284 (11809) *********************** 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 188 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.947 Fit side-chains REVERT: A 246 ILE cc_start: 0.7894 (mp) cc_final: 0.7619 (mt) REVERT: A 544 TYR cc_start: 0.7844 (m-80) cc_final: 0.7491 (m-80) REVERT: B 35 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7191 (mtm-85) REVERT: B 242 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7116 (mm-30) REVERT: E 95 TYR cc_start: 0.8367 (m-80) cc_final: 0.7998 (m-80) outliers start: 27 outliers final: 7 residues processed: 180 average time/residue: 1.3454 time to fit residues: 261.3611 Evaluate side-chains 168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain B residue 236 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.160811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.140669 restraints weight = 11788.157| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.82 r_work: 0.3733 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8667 Z= 0.142 Angle : 0.593 8.183 11815 Z= 0.305 Chirality : 0.043 0.185 1376 Planarity : 0.004 0.043 1490 Dihedral : 4.549 21.731 1221 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 2.20 % Allowed : 20.00 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1105 helix: 0.94 (0.28), residues: 385 sheet: -0.12 (0.30), residues: 272 loop : -0.93 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 169 HIS 0.008 0.002 HIS B 82 PHE 0.018 0.002 PHE B 84 TYR 0.020 0.002 TYR A 534 ARG 0.008 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 397) hydrogen bonds : angle 4.72210 ( 1122) SS BOND : bond 0.00376 ( 3) SS BOND : angle 0.52197 ( 6) covalent geometry : bond 0.00326 ( 8664) covalent geometry : angle 0.59261 (11809) *********************** 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 177 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 2.657 Fit side-chains REVERT: A 246 ILE cc_start: 0.7945 (mp) cc_final: 0.7649 (mt) REVERT: A 544 TYR cc_start: 0.7839 (m-80) cc_final: 0.7486 (m-80) REVERT: B 35 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7201 (mtm-85) REVERT: B 242 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7124 (mm-30) REVERT: C 219 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6575 (mtm180) REVERT: E 95 TYR cc_start: 0.8376 (m-80) cc_final: 0.8011 (m-80) outliers start: 19 outliers final: 9 residues processed: 167 average time/residue: 1.6486 time to fit residues: 295.1563 Evaluate side-chains 168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 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 219 ARG Chi-restraints excluded: chain C residue 263 THR 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 104 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.161034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140851 restraints weight = 11970.151| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.82 r_work: 0.3737 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8667 Z= 0.135 Angle : 0.590 7.570 11815 Z= 0.301 Chirality : 0.043 0.177 1376 Planarity : 0.004 0.043 1490 Dihedral : 4.535 20.631 1221 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 2.77 % Allowed : 20.69 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1105 helix: 0.87 (0.27), residues: 387 sheet: -0.10 (0.31), residues: 272 loop : -0.96 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 169 HIS 0.008 0.002 HIS B 82 PHE 0.018 0.002 PHE B 84 TYR 0.017 0.002 TYR A 176 ARG 0.010 0.001 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 397) hydrogen bonds : angle 4.69410 ( 1122) SS BOND : bond 0.00386 ( 3) SS BOND : angle 0.62423 ( 6) covalent geometry : bond 0.00306 ( 8664) covalent geometry : angle 0.58969 (11809) *********************** 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 182 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.899 Fit side-chains REVERT: A 246 ILE cc_start: 0.7935 (mp) cc_final: 0.7644 (mt) REVERT: B 35 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7196 (mtm-85) REVERT: B 242 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7164 (mm-30) REVERT: C 219 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6546 (mtm180) REVERT: E 95 TYR cc_start: 0.8341 (m-80) cc_final: 0.7669 (m-80) outliers start: 24 outliers final: 13 residues processed: 167 average time/residue: 0.9761 time to fit residues: 175.8502 Evaluate side-chains 170 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 219 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 69 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 101 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.160581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.140405 restraints weight = 11867.629| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.81 r_work: 0.3736 rms_B_bonded: 2.36 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: 0.7325 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8667 Z= 0.153 Angle : 0.608 8.196 11815 Z= 0.313 Chirality : 0.044 0.185 1376 Planarity : 0.004 0.045 1490 Dihedral : 4.568 20.810 1221 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.89 % Favored : 95.02 % Rotamer: Outliers : 1.73 % Allowed : 21.73 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1105 helix: 0.85 (0.27), residues: 387 sheet: -0.12 (0.31), residues: 272 loop : -0.95 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 144 HIS 0.008 0.002 HIS B 82 PHE 0.026 0.002 PHE A 222 TYR 0.018 0.002 TYR A 534 ARG 0.007 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 397) hydrogen bonds : angle 4.70229 ( 1122) SS BOND : bond 0.00403 ( 3) SS BOND : angle 0.56805 ( 6) covalent geometry : bond 0.00353 ( 8664) covalent geometry : angle 0.60819 (11809) *********************** 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 172 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.909 Fit side-chains REVERT: A 246 ILE cc_start: 0.7945 (mp) cc_final: 0.7659 (mt) REVERT: B 35 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7219 (mtm-85) REVERT: B 242 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7070 (mm-30) REVERT: C 219 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6599 (mtm180) REVERT: E 95 TYR cc_start: 0.8335 (m-80) cc_final: 0.7659 (m-80) outliers start: 15 outliers final: 14 residues processed: 161 average time/residue: 1.0064 time to fit residues: 174.5128 Evaluate side-chains 172 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 219 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 69 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 Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 93 optimal weight: 0.0030 chunk 92 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.160579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.140670 restraints weight = 11814.704| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.74 r_work: 0.3738 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2241 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= 0.149 Angle : 0.603 7.389 11815 Z= 0.310 Chirality : 0.043 0.174 1376 Planarity : 0.004 0.046 1490 Dihedral : 4.568 20.770 1221 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 1.85 % Allowed : 21.62 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1105 helix: 0.87 (0.27), residues: 387 sheet: -0.11 (0.31), residues: 273 loop : -0.95 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 144 HIS 0.009 0.002 HIS B 82 PHE 0.020 0.002 PHE C 335 TYR 0.018 0.002 TYR A 534 ARG 0.006 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 397) hydrogen bonds : angle 4.70195 ( 1122) SS BOND : bond 0.00348 ( 3) SS BOND : angle 0.44043 ( 6) covalent geometry : bond 0.00341 ( 8664) covalent geometry : angle 0.60263 (11809) ********************** 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 174 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.853 Fit side-chains REVERT: A 246 ILE cc_start: 0.7904 (mp) cc_final: 0.7628 (mt) REVERT: B 35 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7232 (mtm-85) REVERT: B 242 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7099 (mm-30) REVERT: C 219 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6574 (mtm180) REVERT: E 95 TYR cc_start: 0.8375 (m-80) cc_final: 0.8042 (m-80) outliers start: 16 outliers final: 13 residues processed: 163 average time/residue: 0.9902 time to fit residues: 173.8787 Evaluate side-chains 172 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 219 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 69 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 97 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.159371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139376 restraints weight = 11951.606| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.75 r_work: 0.3721 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8667 Z= 0.193 Angle : 0.643 8.968 11815 Z= 0.331 Chirality : 0.045 0.189 1376 Planarity : 0.004 0.047 1490 Dihedral : 4.670 21.339 1221 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 1.85 % Allowed : 21.39 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1105 helix: 0.79 (0.27), residues: 387 sheet: -0.15 (0.31), residues: 275 loop : -0.96 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 129 HIS 0.009 0.002 HIS B 82 PHE 0.032 0.002 PHE A 222 TYR 0.018 0.002 TYR A 534 ARG 0.006 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 397) hydrogen bonds : angle 4.76261 ( 1122) SS BOND : bond 0.00388 ( 3) SS BOND : angle 0.50855 ( 6) covalent geometry : bond 0.00448 ( 8664) covalent geometry : angle 0.64261 (11809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7384.28 seconds wall clock time: 129 minutes 22.88 seconds (7762.88 seconds total)