Starting phenix.real_space_refine on Tue Feb 3 23:51:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iac_4435/02_2026/6iac_4435.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iac_4435/02_2026/6iac_4435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6iac_4435/02_2026/6iac_4435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iac_4435/02_2026/6iac_4435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iac_4435/02_2026/6iac_4435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iac_4435/02_2026/6iac_4435.map" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 5208 2.51 5 N 1384 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8210 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2353 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1763 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1164 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 135} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1259 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "F" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1019 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 6, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "J" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 6, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "K" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 112 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 6, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 1.61, per 1000 atoms: 0.20 Number of scatterers: 8210 At special positions: 0 Unit cell: (126.497, 184.962, 255.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1595 8.00 N 1384 7.00 C 5208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 194.5 milliseconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 61.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 4.322A pdb=" N VAL A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 152 through 177 removed outlier: 3.960A pdb=" N ILE A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 227 through 247 removed outlier: 4.174A pdb=" N THR A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.522A pdb=" N GLY A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.567A pdb=" N THR A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.653A pdb=" N PHE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.721A pdb=" N ASP A 324 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.583A pdb=" N LYS B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 removed outlier: 3.585A pdb=" N LYS B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 68 through 79 removed outlier: 3.651A pdb=" N LEU B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.562A pdb=" N ILE B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.567A pdb=" N LYS B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 4.109A pdb=" N GLU B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 removed outlier: 3.626A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 19 " --> pdb=" O ARG D 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 14 through 19' Processing helix chain 'D' and resid 20 through 23 removed outlier: 3.840A pdb=" N LYS D 23 " --> pdb=" O GLU D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 42 through 53 removed outlier: 3.550A pdb=" N ARG D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 84 removed outlier: 4.089A pdb=" N ALA D 60 " --> pdb=" O ILE D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 removed outlier: 4.946A pdb=" N ASP D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 141 removed outlier: 3.939A pdb=" N ILE D 104 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP D 140 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.335A pdb=" N ILE D 145 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D 146 " --> pdb=" O LYS D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'E' and resid 14 through 17 Processing helix chain 'E' and resid 18 through 27 removed outlier: 3.772A pdb=" N TYR E 22 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU E 26 " --> pdb=" O TYR E 22 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 65 removed outlier: 3.722A pdb=" N LYS E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU E 55 " --> pdb=" O ARG E 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 74 removed outlier: 4.097A pdb=" N GLU E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 104 removed outlier: 4.129A pdb=" N ASP E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Proline residue: E 85 - end of helix removed outlier: 3.719A pdb=" N TRP E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 96 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP E 98 " --> pdb=" O GLY E 94 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 101 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP E 102 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 146 removed outlier: 3.670A pdb=" N LYS E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 119 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'F' and resid 44 through 83 removed outlier: 3.960A pdb=" N LYS F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP F 79 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.713A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 110 through 135 removed outlier: 3.517A pdb=" N ALA F 114 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 removed outlier: 3.923A pdb=" N LYS F 139 " --> pdb=" O SER F 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'G' and resid 78 through 94 Processing helix chain 'H' and resid 78 through 94 Processing helix chain 'I' and resid 78 through 98 Processing helix chain 'J' and resid 78 through 97 removed outlier: 3.599A pdb=" N GLN J 97 " --> pdb=" O PHE J 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 94 Processing helix chain 'L' and resid 78 through 95 removed outlier: 3.508A pdb=" N PHE L 93 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.984A pdb=" N VAL A 68 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 removed outlier: 4.017A pdb=" N SER A 181 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 127 removed outlier: 3.779A pdb=" N GLN B 125 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.500A pdb=" N ARG B 206 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 135 through 139 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 435 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.69 Time building geometry restraints manager: 0.73 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: 2182 1.33 - 1.45: 1673 1.45 - 1.57: 4450 1.57 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 8348 Sorted by residual: bond pdb=" C ARG D 15 " pdb=" N PRO D 16 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.71e+01 bond pdb=" C GLU A 286 " pdb=" N PRO A 287 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.08e-02 8.57e+03 1.58e+01 bond pdb=" CA ASP A 153 " pdb=" C ASP A 153 " ideal model delta sigma weight residual 1.523 1.570 -0.046 1.80e-02 3.09e+03 6.65e+00 bond pdb=" CB MET B 6 " pdb=" CG MET B 6 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.09e+00 bond pdb=" CB TYR A 45 " pdb=" CG TYR A 45 " ideal model delta sigma weight residual 1.512 1.461 0.051 2.20e-02 2.07e+03 5.44e+00 ... (remaining 8343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 10997 3.58 - 7.16: 225 7.16 - 10.74: 42 10.74 - 14.32: 5 14.32 - 17.90: 2 Bond angle restraints: 11271 Sorted by residual: angle pdb=" C THR A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C LYS D 89 " pdb=" N ASP D 90 " pdb=" CA ASP D 90 " ideal model delta sigma weight residual 121.54 132.27 -10.73 1.91e+00 2.74e-01 3.15e+01 angle pdb=" CA TYR A 45 " pdb=" CB TYR A 45 " pdb=" CG TYR A 45 " ideal model delta sigma weight residual 113.90 123.83 -9.93 1.80e+00 3.09e-01 3.04e+01 angle pdb=" C ASP A 153 " pdb=" CA ASP A 153 " pdb=" CB ASP A 153 " ideal model delta sigma weight residual 110.36 100.37 9.99 1.85e+00 2.92e-01 2.92e+01 angle pdb=" C ASP A 264 " pdb=" N GLU A 265 " pdb=" CA GLU A 265 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 ... (remaining 11266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4589 16.07 - 32.14: 371 32.14 - 48.21: 78 48.21 - 64.28: 1 64.28 - 80.34: 6 Dihedral angle restraints: 5045 sinusoidal: 1896 harmonic: 3149 Sorted by residual: dihedral pdb=" CA GLU A 187 " pdb=" C GLU A 187 " pdb=" N ILE A 188 " pdb=" CA ILE A 188 " ideal model delta harmonic sigma weight residual -180.00 -139.12 -40.88 0 5.00e+00 4.00e-02 6.68e+01 dihedral pdb=" CA SER B 114 " pdb=" C SER B 114 " pdb=" N SER B 115 " pdb=" CA SER B 115 " ideal model delta harmonic sigma weight residual -180.00 -141.37 -38.63 0 5.00e+00 4.00e-02 5.97e+01 dihedral pdb=" CA TYR B 113 " pdb=" C TYR B 113 " pdb=" N SER B 114 " pdb=" CA SER B 114 " ideal model delta harmonic sigma weight residual 180.00 143.38 36.62 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 5042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 997 0.079 - 0.158: 210 0.158 - 0.237: 40 0.237 - 0.316: 6 0.316 - 0.395: 2 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA TYR A 45 " pdb=" N TYR A 45 " pdb=" C TYR A 45 " pdb=" CB TYR A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CG LEU A 8 " pdb=" CB LEU A 8 " pdb=" CD1 LEU A 8 " pdb=" CD2 LEU A 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB THR A 46 " pdb=" CA THR A 46 " pdb=" OG1 THR A 46 " pdb=" CG2 THR A 46 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1252 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 90 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C ASP D 90 " -0.070 2.00e-02 2.50e+03 pdb=" O ASP D 90 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU D 91 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 46 " -0.034 2.00e-02 2.50e+03 2.77e-02 1.53e+01 pdb=" CG TYR F 46 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR F 46 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR F 46 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 46 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR F 46 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR F 46 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 46 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 45 " -0.035 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR A 45 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR A 45 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 45 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 45 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 45 " 0.003 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2080 2.78 - 3.31: 7828 3.31 - 3.84: 12670 3.84 - 4.37: 13537 4.37 - 4.90: 22438 Nonbonded interactions: 58553 Sorted by model distance: nonbonded pdb=" O ILE A 157 " pdb=" OG1 THR A 161 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 292 " pdb=" O LEU A 297 " model vdw 2.261 3.040 nonbonded pdb=" O PHE A 273 " pdb=" OG SER A 276 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR D 66 " pdb=" OD1 ASP F 67 " model vdw 2.314 3.040 nonbonded pdb=" O THR A 108 " pdb=" OH TYR A 132 " model vdw 2.318 3.040 ... (remaining 58548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 24 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 34 or (resid 35 throu \ gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 144)) selection = (chain 'E' and (resid 24 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 34 or (resid 35 throu \ gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or r \ esid 52 through 105 or (resid 106 through 107 and (name N or name CA or name C o \ r name O or name CB )) or resid 108 through 110 or (resid 111 and (name N or nam \ e CA or name C or name O or name CB )) or resid 112 through 144)) selection = (chain 'F' and (resid 24 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 50 or (resid 51 and (name N or nam \ e CA or name C or name O or name CB )) or resid 52 through 105 or (resid 106 thr \ ough 107 and (name N or name CA or name C or name O or name CB )) or resid 108 t \ hrough 110 or (resid 111 and (name N or name CA or name C or name O or name CB ) \ ) or resid 112 through 144)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 77 through 98) selection = (chain 'J' and resid 77 through 98) selection = (chain 'K' and (name N or name CA or name C or name O or name CB )) selection = (chain 'L' and resid 77 through 98) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.780 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.009 0.082 8348 Z= 0.426 Angle : 1.315 17.897 11271 Z= 0.721 Chirality : 0.069 0.395 1255 Planarity : 0.007 0.073 1460 Dihedral : 12.355 80.344 2989 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.95 % Favored : 87.85 % Rotamer: Outliers : 1.10 % Allowed : 6.11 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.78 % 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: -4.54 (0.20), residues: 1029 helix: -2.28 (0.16), residues: 582 sheet: -3.46 (0.43), residues: 84 loop : -3.95 (0.27), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 24 TYR 0.066 0.005 TYR A 45 PHE 0.064 0.005 PHE D 31 TRP 0.026 0.004 TRP F 95 HIS 0.021 0.006 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00943 ( 8348) covalent geometry : angle 1.31470 (11271) hydrogen bonds : bond 0.16551 ( 435) hydrogen bonds : angle 7.28134 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 417 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 77 GLN cc_start: 0.9381 (mp10) cc_final: 0.9031 (mp10) REVERT: A 185 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7686 (ttmt) REVERT: A 201 TYR cc_start: 0.9084 (t80) cc_final: 0.8456 (t80) REVERT: A 241 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8345 (tppt) REVERT: A 244 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 248 TYR cc_start: 0.8663 (t80) cc_final: 0.8438 (t80) REVERT: A 259 GLU cc_start: 0.7944 (mp0) cc_final: 0.7744 (mp0) REVERT: A 303 TYR cc_start: 0.8184 (t80) cc_final: 0.7851 (t80) REVERT: A 306 GLU cc_start: 0.6681 (pt0) cc_final: 0.6439 (pt0) REVERT: B 18 LYS cc_start: 0.9060 (tmmm) cc_final: 0.8793 (ttpt) REVERT: B 47 ASP cc_start: 0.8620 (p0) cc_final: 0.8162 (p0) REVERT: B 51 LEU cc_start: 0.9506 (tp) cc_final: 0.9250 (tp) REVERT: B 80 HIS cc_start: 0.8830 (t-90) cc_final: 0.8628 (t-90) REVERT: B 125 GLN cc_start: 0.8587 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 145 ASN cc_start: 0.8448 (t0) cc_final: 0.8204 (t0) REVERT: B 188 ASP cc_start: 0.8873 (p0) cc_final: 0.8222 (m-30) REVERT: B 250 ILE cc_start: 0.8450 (tp) cc_final: 0.8176 (tt) REVERT: D 25 ARG cc_start: 0.8125 (ttt180) cc_final: 0.7588 (mpp-170) REVERT: D 38 TYR cc_start: 0.8652 (m-80) cc_final: 0.8447 (m-80) REVERT: D 47 ASP cc_start: 0.7655 (t0) cc_final: 0.7420 (t0) REVERT: D 75 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7705 (mmpt) REVERT: D 87 GLN cc_start: 0.9137 (mt0) cc_final: 0.8905 (mt0) REVERT: D 90 ASP cc_start: 0.7751 (t0) cc_final: 0.7465 (p0) REVERT: D 133 ASP cc_start: 0.8682 (t0) cc_final: 0.8318 (t70) REVERT: E 14 ILE cc_start: 0.8274 (mm) cc_final: 0.7958 (pt) REVERT: E 17 PHE cc_start: 0.9141 (m-80) cc_final: 0.8863 (m-10) REVERT: E 22 TYR cc_start: 0.8511 (t80) cc_final: 0.7942 (t80) REVERT: E 23 LYS cc_start: 0.9392 (tptp) cc_final: 0.9189 (tptt) REVERT: E 51 ARG cc_start: 0.7862 (tpt-90) cc_final: 0.7403 (tmt170) REVERT: E 86 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8593 (tm-30) REVERT: E 90 ASP cc_start: 0.8850 (t0) cc_final: 0.8375 (m-30) REVERT: E 104 ILE cc_start: 0.8808 (mt) cc_final: 0.7932 (mm) REVERT: F 27 ARG cc_start: 0.8032 (ptp90) cc_final: 0.7751 (tpt-90) REVERT: F 43 LYS cc_start: 0.8892 (mtpm) cc_final: 0.8339 (mptt) REVERT: F 54 LYS cc_start: 0.6338 (tmmt) cc_final: 0.5470 (mttt) REVERT: F 57 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8380 (tm-30) REVERT: F 68 ASN cc_start: 0.8697 (t0) cc_final: 0.8437 (t0) REVERT: F 87 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8150 (tp-100) REVERT: F 91 LEU cc_start: 0.7608 (pp) cc_final: 0.6592 (pp) REVERT: F 123 PHE cc_start: 0.7056 (t80) cc_final: 0.6730 (t80) REVERT: F 125 VAL cc_start: 0.9406 (t) cc_final: 0.9038 (p) REVERT: F 143 LYS cc_start: 0.5689 (mppt) cc_final: 0.4090 (mmtt) outliers start: 9 outliers final: 2 residues processed: 420 average time/residue: 0.0879 time to fit residues: 48.4965 Evaluate side-chains 310 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS E 6 ASN E 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.154256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130161 restraints weight = 18778.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132499 restraints weight = 9540.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133850 restraints weight = 5747.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134800 restraints weight = 4060.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135463 restraints weight = 3187.259| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8348 Z= 0.148 Angle : 0.769 12.088 11271 Z= 0.408 Chirality : 0.047 0.222 1255 Planarity : 0.005 0.049 1460 Dihedral : 6.599 36.183 1138 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.77 % Allowed : 17.36 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.60 (0.24), residues: 1029 helix: -0.42 (0.20), residues: 593 sheet: -3.26 (0.47), residues: 69 loop : -3.62 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 285 TYR 0.025 0.002 TYR A 45 PHE 0.026 0.002 PHE F 84 TRP 0.014 0.001 TRP F 95 HIS 0.004 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8348) covalent geometry : angle 0.76854 (11271) hydrogen bonds : bond 0.03945 ( 435) hydrogen bonds : angle 4.80446 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 356 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 26 ARG cc_start: 0.9090 (ttp-170) cc_final: 0.7907 (ttp-170) REVERT: A 45 TYR cc_start: 0.8788 (p90) cc_final: 0.7403 (p90) REVERT: A 57 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 74 ARG cc_start: 0.6824 (mmp-170) cc_final: 0.6593 (tpt-90) REVERT: A 76 LYS cc_start: 0.8583 (pttt) cc_final: 0.8186 (ptmt) REVERT: A 185 LYS cc_start: 0.7622 (ttmt) cc_final: 0.6912 (tmtt) REVERT: A 189 ASN cc_start: 0.7009 (m-40) cc_final: 0.6695 (m-40) REVERT: A 214 ASN cc_start: 0.6535 (m110) cc_final: 0.6304 (m110) REVERT: A 248 TYR cc_start: 0.8485 (t80) cc_final: 0.8154 (t80) REVERT: A 259 GLU cc_start: 0.7646 (mp0) cc_final: 0.7178 (mp0) REVERT: A 303 TYR cc_start: 0.7788 (t80) cc_final: 0.7453 (t80) REVERT: B 38 GLN cc_start: 0.7865 (pm20) cc_final: 0.7358 (pt0) REVERT: B 188 ASP cc_start: 0.8604 (p0) cc_final: 0.8397 (m-30) REVERT: D 25 ARG cc_start: 0.8069 (ttt180) cc_final: 0.7436 (mpp-170) REVERT: D 47 ASP cc_start: 0.7359 (t0) cc_final: 0.7154 (t0) REVERT: D 96 LEU cc_start: 0.7069 (pp) cc_final: 0.6570 (pp) REVERT: D 122 LEU cc_start: 0.9074 (pp) cc_final: 0.8654 (mp) REVERT: D 141 LEU cc_start: 0.8840 (mt) cc_final: 0.8527 (pp) REVERT: E 22 TYR cc_start: 0.8436 (t80) cc_final: 0.7809 (t80) REVERT: E 46 TYR cc_start: 0.9167 (t80) cc_final: 0.8632 (t80) REVERT: E 78 ASP cc_start: 0.8512 (m-30) cc_final: 0.7929 (t0) REVERT: E 86 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8499 (tm-30) REVERT: F 27 ARG cc_start: 0.8062 (ptp90) cc_final: 0.7631 (tpt-90) REVERT: F 43 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8300 (mptt) REVERT: F 54 LYS cc_start: 0.6738 (tmmt) cc_final: 0.6100 (mttt) REVERT: F 57 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8096 (tm-30) REVERT: F 78 ASP cc_start: 0.7832 (m-30) cc_final: 0.7517 (m-30) REVERT: F 87 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8029 (tp-100) REVERT: F 91 LEU cc_start: 0.7566 (pp) cc_final: 0.6570 (pp) REVERT: F 116 LEU cc_start: 0.9166 (mt) cc_final: 0.8891 (mt) REVERT: F 125 VAL cc_start: 0.9347 (t) cc_final: 0.8959 (t) REVERT: F 129 LYS cc_start: 0.9245 (pttp) cc_final: 0.9035 (mmtm) REVERT: F 143 LYS cc_start: 0.5649 (mppt) cc_final: 0.3675 (mmtt) outliers start: 39 outliers final: 20 residues processed: 371 average time/residue: 0.0834 time to fit residues: 40.9383 Evaluate side-chains 317 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 296 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128972 restraints weight = 18905.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131179 restraints weight = 9531.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132635 restraints weight = 5781.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133582 restraints weight = 4039.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133891 restraints weight = 3153.780| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8348 Z= 0.148 Angle : 0.749 10.858 11271 Z= 0.390 Chirality : 0.047 0.251 1255 Planarity : 0.004 0.041 1460 Dihedral : 5.938 35.435 1136 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 6.60 % Allowed : 18.70 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.75 (0.26), residues: 1029 helix: 0.39 (0.21), residues: 596 sheet: -2.91 (0.50), residues: 69 loop : -3.53 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 285 TYR 0.030 0.002 TYR E 45 PHE 0.023 0.002 PHE E 74 TRP 0.014 0.001 TRP F 95 HIS 0.010 0.002 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8348) covalent geometry : angle 0.74875 (11271) hydrogen bonds : bond 0.03447 ( 435) hydrogen bonds : angle 4.46177 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.2576 (ptt-90) cc_final: 0.2337 (ptt-90) REVERT: A 45 TYR cc_start: 0.8819 (p90) cc_final: 0.7920 (p90) REVERT: A 57 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 163 GLU cc_start: 0.8002 (tt0) cc_final: 0.7759 (tt0) REVERT: A 189 ASN cc_start: 0.7063 (m-40) cc_final: 0.6776 (m-40) REVERT: B 23 GLU cc_start: 0.8139 (pm20) cc_final: 0.7199 (pt0) REVERT: B 30 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8390 (mm) REVERT: B 188 ASP cc_start: 0.8618 (p0) cc_final: 0.8372 (m-30) REVERT: B 229 ASP cc_start: 0.7685 (t0) cc_final: 0.7482 (t0) REVERT: D 25 ARG cc_start: 0.8101 (ttt180) cc_final: 0.7390 (mpp-170) REVERT: D 38 TYR cc_start: 0.8815 (m-80) cc_final: 0.8603 (m-80) REVERT: D 122 LEU cc_start: 0.9033 (pp) cc_final: 0.8628 (mp) REVERT: E 78 ASP cc_start: 0.8516 (m-30) cc_final: 0.7970 (t0) REVERT: F 27 ARG cc_start: 0.8159 (ptp90) cc_final: 0.7606 (tpt-90) REVERT: F 41 ASN cc_start: 0.8880 (m110) cc_final: 0.8512 (m110) REVERT: F 54 LYS cc_start: 0.6761 (tmmt) cc_final: 0.6071 (mttt) REVERT: F 57 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8183 (tm-30) REVERT: F 87 GLN cc_start: 0.8485 (tp-100) cc_final: 0.8008 (tp-100) REVERT: F 91 LEU cc_start: 0.7612 (pp) cc_final: 0.6624 (pp) REVERT: F 131 MET cc_start: 0.7301 (mmm) cc_final: 0.6974 (mmp) outliers start: 54 outliers final: 34 residues processed: 337 average time/residue: 0.0771 time to fit residues: 36.1609 Evaluate side-chains 333 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.781 > 50: distance: 16 - 118: 18.292 distance: 27 - 105: 12.682 distance: 30 - 102: 15.243 distance: 60 - 65: 13.462 distance: 65 - 66: 16.828 distance: 66 - 67: 13.682 distance: 66 - 69: 15.723 distance: 67 - 68: 9.738 distance: 67 - 70: 12.562 distance: 70 - 71: 16.248 distance: 71 - 72: 18.276 distance: 71 - 74: 15.974 distance: 72 - 73: 15.232 distance: 72 - 78: 33.424 distance: 74 - 75: 13.843 distance: 75 - 76: 8.891 distance: 75 - 77: 3.173 distance: 78 - 79: 13.427 distance: 79 - 80: 17.804 distance: 79 - 82: 9.262 distance: 80 - 81: 14.317 distance: 80 - 86: 14.522 distance: 82 - 83: 6.935 distance: 83 - 84: 7.266 distance: 83 - 85: 5.644 distance: 86 - 87: 7.148 distance: 87 - 88: 9.755 distance: 87 - 90: 13.825 distance: 88 - 89: 15.378 distance: 88 - 94: 19.429 distance: 90 - 91: 9.243 distance: 91 - 92: 10.567 distance: 91 - 93: 6.880 distance: 94 - 95: 6.857 distance: 95 - 96: 9.969 distance: 95 - 98: 10.734 distance: 96 - 97: 12.238 distance: 96 - 102: 15.556 distance: 98 - 99: 24.948 distance: 98 - 100: 13.492 distance: 99 - 101: 8.733 distance: 102 - 103: 17.302 distance: 103 - 104: 11.764 distance: 103 - 106: 7.451 distance: 104 - 105: 13.272 distance: 104 - 110: 16.607 distance: 106 - 107: 11.411 distance: 106 - 108: 14.406 distance: 107 - 109: 11.107 distance: 110 - 111: 10.344 distance: 111 - 114: 6.429 distance: 112 - 113: 9.696 distance: 112 - 118: 11.339 distance: 114 - 115: 13.631 distance: 115 - 116: 12.934 distance: 115 - 117: 12.973 distance: 118 - 119: 40.333 distance: 119 - 120: 35.016 distance: 119 - 122: 25.955 distance: 120 - 121: 17.614 distance: 120 - 126: 30.510 distance: 122 - 123: 10.459 distance: 123 - 124: 10.489 distance: 123 - 125: 23.354 distance: 126 - 127: 37.839 distance: 127 - 128: 25.295 distance: 127 - 130: 24.985 distance: 128 - 129: 17.042 distance: 128 - 133: 42.241 distance: 130 - 131: 10.714 distance: 130 - 132: 17.563 distance: 133 - 134: 27.865 distance: 134 - 135: 25.291 distance: 134 - 137: 34.780 distance: 135 - 136: 10.036 distance: 135 - 139: 13.032 distance: 137 - 138: 22.434