Starting phenix.real_space_refine on Sat Dec 20 21:46:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ezo_4162/12_2025/6ezo_4162.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ezo_4162/12_2025/6ezo_4162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ezo_4162/12_2025/6ezo_4162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ezo_4162/12_2025/6ezo_4162.map" model { file = "/net/cci-nas-00/data/ceres_data/6ezo_4162/12_2025/6ezo_4162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ezo_4162/12_2025/6ezo_4162.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 24 5.16 5 Cl 2 4.86 5 C 11676 2.51 5 N 3558 2.21 5 O 3498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18758 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1624 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 558 Unresolved non-hydrogen angles: 690 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLU:plan': 17, 'PHE:plan': 7, 'GLN:plan1': 6, 'ASP:plan': 13, 'ARG:plan': 12, 'ASN:plan1': 7, 'TYR:plan': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 290 Chain: "B" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1627 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 459 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLU:plan': 17, 'PHE:plan': 6, 'GLN:plan1': 7, 'ASP:plan': 13, 'ARG:plan': 12, 'ASN:plan1': 7, 'TYR:plan': 4, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 299 Chain: "C" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 1857 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 291} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 550 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLU:plan': 31, 'ARG:plan': 15, 'GLN:plan1': 6, 'ASP:plan': 7, 'HIS:plan': 2, 'ASN:plan1': 10, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 297 Chain: "D" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 1816 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 756 Unresolved non-hydrogen dihedrals: 463 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLU:plan': 32, 'ARG:plan': 17, 'GLN:plan1': 7, 'ASP:plan': 7, 'HIS:plan': 3, 'ASN:plan1': 10, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 326 Chain: "E" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 1812 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 280} Link IDs: {'PTRANS': 12, 'TRANS': 334} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 881 Unresolved non-hydrogen angles: 1107 Unresolved non-hydrogen dihedrals: 684 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLU:plan': 20, 'GLN:plan1': 8, 'ARG:plan': 17, 'ASP:plan': 22, 'ASN:plan1': 11, 'TYR:plan': 4, 'PHE:plan': 4, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 373 Chain: "F" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 1806 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'PTRANS': 12, 'TRANS': 334} Chain breaks: 3 Unresolved non-hydrogen bonds: 888 Unresolved non-hydrogen angles: 1116 Unresolved non-hydrogen dihedrals: 692 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLU:plan': 20, 'GLN:plan1': 8, 'ARG:plan': 17, 'ASP:plan': 22, 'ASN:plan1': 11, 'TYR:plan': 4, 'PHE:plan': 5, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 379 Chain: "G" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2013 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PTRANS': 18, 'TRANS': 336} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 764 Unresolved non-hydrogen angles: 969 Unresolved non-hydrogen dihedrals: 580 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 20, 'ASP:plan': 13, 'ASN:plan1': 13, 'PHE:plan': 2, 'HIS:plan': 3, 'TYR:plan': 2, 'GLU:plan': 18} Unresolved non-hydrogen planarities: 355 Chain: "H" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1993 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 256} Link IDs: {'PTRANS': 18, 'TRANS': 334} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 769 Unresolved non-hydrogen angles: 976 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 21, 'ASP:plan': 13, 'ASN:plan1': 13, 'PHE:plan': 2, 'HIS:plan': 4, 'GLU:plan': 18, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 358 Chain: "I" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2117 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 315} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 375} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1318 Unresolved non-hydrogen dihedrals: 801 Unresolved non-hydrogen chiralities: 132 Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 13, 'ASP:plan': 18, 'ARG:plan': 21, 'ASN:plan1': 19, 'PHE:plan': 10, 'TRP:plan': 2, 'HIS:plan': 12, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 525 Chain: "J" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2063 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 323} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 375} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1062 Unresolved non-hydrogen angles: 1369 Unresolved non-hydrogen dihedrals: 838 Unresolved non-hydrogen chiralities: 132 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 19, 'ARG:plan': 25, 'ASN:plan1': 19, 'GLU:plan': 20, 'PHE:plan': 9, 'TRP:plan': 2, 'HIS:plan': 12, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 552 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.45, per 1000 atoms: 0.24 Number of scatterers: 18758 At special positions: 0 Unit cell: (169.75, 131.25, 147, 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 2 17.00 S 24 16.00 O 3498 8.00 N 3558 7.00 C 11676 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: 1.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6366 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 33 sheets defined 32.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 6 through 16 removed outlier: 3.751A pdb=" N GLU A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.543A pdb=" N ALA A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 78 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 91 through 106 removed outlier: 4.174A pdb=" N GLU A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 removed outlier: 4.179A pdb=" N LYS A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.744A pdb=" N LEU A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.776A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 removed outlier: 3.999A pdb=" N GLU A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 removed outlier: 4.391A pdb=" N CYS A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'B' and resid 7 through 16 removed outlier: 3.750A pdb=" N GLU B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 41 through 57 removed outlier: 4.021A pdb=" N LEU B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 78 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 91 through 106 removed outlier: 4.175A pdb=" N GLU B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 4.182A pdb=" N LYS B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 131 through 143 removed outlier: 3.739A pdb=" N LEU B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.778A pdb=" N MET B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 188 removed outlier: 4.001A pdb=" N GLU B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 4.392A pdb=" N CYS B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.930A pdb=" N LEU B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 25 removed outlier: 3.837A pdb=" N SER C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 23 " --> pdb=" O VAL C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 48 Processing helix chain 'C' and resid 55 through 69 Processing helix chain 'C' and resid 75 through 96 removed outlier: 4.256A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.567A pdb=" N ASN C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 152 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLN C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 180 Processing helix chain 'C' and resid 200 through 209 removed outlier: 4.125A pdb=" N ALA C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.883A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 25 removed outlier: 3.836A pdb=" N SER D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 48 Processing helix chain 'D' and resid 55 through 69 Processing helix chain 'D' and resid 75 through 96 removed outlier: 4.241A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 145 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.565A pdb=" N ASN D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA D 152 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 200 through 209 removed outlier: 3.974A pdb=" N ALA D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.882A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 87 through 93 removed outlier: 4.115A pdb=" N ILE E 93 " --> pdb=" O SER E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 123 removed outlier: 4.623A pdb=" N PHE E 121 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 209 through 214 removed outlier: 4.063A pdb=" N ASP E 213 " --> pdb=" O LYS E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 227 removed outlier: 3.546A pdb=" N GLU E 227 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 320 through 324 removed outlier: 4.479A pdb=" N ASN E 323 " --> pdb=" O MET E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 87 through 93 removed outlier: 4.115A pdb=" N ILE F 93 " --> pdb=" O SER F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 123 removed outlier: 4.620A pdb=" N PHE F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 209 through 214 removed outlier: 4.064A pdb=" N ASP F 213 " --> pdb=" O LYS F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 227 removed outlier: 3.545A pdb=" N GLU F 227 " --> pdb=" O ILE F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 320 through 324 removed outlier: 4.478A pdb=" N ASN F 323 " --> pdb=" O MET F 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 removed outlier: 3.922A pdb=" N LEU G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 238 Processing helix chain 'G' and resid 249 through 256 Processing helix chain 'G' and resid 256 through 267 Processing helix chain 'G' and resid 273 through 286 removed outlier: 3.718A pdb=" N ILE G 277 " --> pdb=" O MET G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 311 removed outlier: 3.909A pdb=" N VAL G 308 " --> pdb=" O ILE G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 322 removed outlier: 3.984A pdb=" N ARG G 321 " --> pdb=" O GLN G 317 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE G 322 " --> pdb=" O ALA G 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 317 through 322' Processing helix chain 'G' and resid 323 through 327 Processing helix chain 'G' and resid 343 through 347 removed outlier: 3.626A pdb=" N LEU G 346 " --> pdb=" O SER G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 374 Processing helix chain 'G' and resid 389 through 391 No H-bonds generated for 'chain 'G' and resid 389 through 391' Processing helix chain 'G' and resid 423 through 427 Processing helix chain 'G' and resid 473 through 479 Processing helix chain 'G' and resid 508 through 512 Processing helix chain 'G' and resid 513 through 518 removed outlier: 3.694A pdb=" N ARG G 517 " --> pdb=" O PRO G 513 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL G 518 " --> pdb=" O VAL G 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 513 through 518' Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.916A pdb=" N GLN H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 removed outlier: 3.921A pdb=" N LEU H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 238 Processing helix chain 'H' and resid 249 through 256 Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 272 through 286 removed outlier: 3.823A pdb=" N ALA H 276 " --> pdb=" O SER H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 311 removed outlier: 3.908A pdb=" N VAL H 308 " --> pdb=" O ILE H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 322 removed outlier: 3.982A pdb=" N ARG H 321 " --> pdb=" O GLN H 317 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 317 through 322' Processing helix chain 'H' and resid 323 through 327 Processing helix chain 'H' and resid 343 through 347 removed outlier: 3.627A pdb=" N LEU H 346 " --> pdb=" O SER H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 374 Processing helix chain 'H' and resid 389 through 391 No H-bonds generated for 'chain 'H' and resid 389 through 391' Processing helix chain 'H' and resid 423 through 427 Processing helix chain 'H' and resid 473 through 477 removed outlier: 3.674A pdb=" N TRP H 476 " --> pdb=" O LEU H 473 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN H 477 " --> pdb=" O ALA H 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 473 through 477' Processing helix chain 'H' and resid 508 through 512 Processing helix chain 'H' and resid 513 through 518 removed outlier: 3.696A pdb=" N ARG H 517 " --> pdb=" O PRO H 513 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 513 through 518' Processing helix chain 'I' and resid 74 through 87 removed outlier: 3.932A pdb=" N TYR I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU I 80 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY I 87 " --> pdb=" O LEU I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 109 removed outlier: 4.196A pdb=" N LEU I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 142 Processing helix chain 'I' and resid 163 through 171 removed outlier: 3.838A pdb=" N GLU I 167 " --> pdb=" O ARG I 163 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG I 171 " --> pdb=" O GLU I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 217 through 221 removed outlier: 4.167A pdb=" N GLY I 220 " --> pdb=" O LYS I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 removed outlier: 4.185A pdb=" N GLN I 232 " --> pdb=" O LEU I 228 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER I 234 " --> pdb=" O LEU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 262 removed outlier: 3.941A pdb=" N GLN I 258 " --> pdb=" O PRO I 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE I 260 " --> pdb=" O VAL I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 276 Processing helix chain 'I' and resid 302 through 310 removed outlier: 3.868A pdb=" N ALA I 308 " --> pdb=" O HIS I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 342 removed outlier: 3.555A pdb=" N ASN I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE I 342 " --> pdb=" O ARG I 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 338 through 342' Processing helix chain 'J' and resid 59 through 63 removed outlier: 3.837A pdb=" N GLN J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 59 through 63' Processing helix chain 'J' and resid 74 through 87 removed outlier: 3.932A pdb=" N TYR J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR J 79 " --> pdb=" O LEU J 75 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU J 80 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 109 removed outlier: 4.197A pdb=" N LEU J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 142 Processing helix chain 'J' and resid 163 through 168 removed outlier: 3.842A pdb=" N GLU J 167 " --> pdb=" O ARG J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 175 Processing helix chain 'J' and resid 217 through 221 removed outlier: 4.170A pdb=" N GLY J 220 " --> pdb=" O LYS J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 234 removed outlier: 4.185A pdb=" N GLN J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 262 removed outlier: 3.945A pdb=" N GLN J 258 " --> pdb=" O PRO J 254 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE J 260 " --> pdb=" O VAL J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 276 Processing helix chain 'J' and resid 302 through 310 removed outlier: 3.867A pdb=" N ALA J 308 " --> pdb=" O HIS J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 342 removed outlier: 3.553A pdb=" N ASN J 341 " --> pdb=" O SER J 338 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE J 342 " --> pdb=" O ARG J 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 338 through 342' Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 127 removed outlier: 6.391A pdb=" N ALA A 123 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR A 151 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 125 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N THR A 176 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 150 " --> pdb=" O THR A 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.846A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.802A pdb=" N GLY A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 206 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 208 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA5, first strand: chain 'B' and resid 123 through 127 removed outlier: 6.394A pdb=" N ALA B 123 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR B 151 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR B 176 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 150 " --> pdb=" O THR B 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 196 removed outlier: 6.847A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 201 removed outlier: 3.804A pdb=" N GLY B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 206 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 208 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AA9, first strand: chain 'C' and resid 213 through 218 removed outlier: 3.745A pdb=" N VAL C 189 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 165 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB2, first strand: chain 'C' and resid 307 through 308 removed outlier: 6.688A pdb=" N SER C 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N LEU G 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 165 through 168 removed outlier: 3.662A pdb=" N ILE D 165 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 189 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 232 through 233 removed outlier: 6.550A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AB6, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.623A pdb=" N SER D 307 " --> pdb=" O TYR H 385 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LEU H 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 52 through 54 removed outlier: 3.727A pdb=" N VAL E 54 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL E 101 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 167 through 170 removed outlier: 5.183A pdb=" N GLY E 159 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE E 193 " --> pdb=" O VAL J 240 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL J 238 " --> pdb=" O PHE E 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 357 through 358 removed outlier: 6.267A pdb=" N LEU E 357 " --> pdb=" O ILE E 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 379 through 380 Processing sheet with id=AC2, first strand: chain 'E' and resid 391 through 392 removed outlier: 6.330A pdb=" N LEU E 391 " --> pdb=" O ILE E 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 52 through 54 removed outlier: 3.728A pdb=" N VAL F 54 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL F 101 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 167 through 170 removed outlier: 5.182A pdb=" N GLY F 159 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 193 " --> pdb=" O VAL I 240 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL I 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 357 through 358 removed outlier: 6.267A pdb=" N LEU F 357 " --> pdb=" O ILE F 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 379 through 381 removed outlier: 6.116A pdb=" N LEU F 380 " --> pdb=" O VAL F 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 391 through 392 removed outlier: 6.329A pdb=" N LEU F 391 " --> pdb=" O ILE F 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'G' and resid 413 through 415 removed outlier: 3.657A pdb=" N ALA G 407 " --> pdb=" O MET G 415 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU G 408 " --> pdb=" O CYS G 444 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 500 through 502 removed outlier: 3.870A pdb=" N GLY G 505 " --> pdb=" O THR G 502 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 413 through 415 removed outlier: 3.662A pdb=" N ALA H 407 " --> pdb=" O MET H 415 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU H 408 " --> pdb=" O CYS H 444 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 500 through 502 removed outlier: 3.871A pdb=" N GLY H 505 " --> pdb=" O THR H 502 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 121 through 124 removed outlier: 5.732A pdb=" N VAL I 93 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL I 46 " --> pdb=" O VAL I 151 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 245 through 252 removed outlier: 6.439A pdb=" N CYS I 247 " --> pdb=" O LYS I 186 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS I 186 " --> pdb=" O CYS I 247 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE I 249 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N THR I 292 " --> pdb=" O MET I 183 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE I 185 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 121 through 124 removed outlier: 5.733A pdb=" N VAL J 93 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL J 46 " --> pdb=" O VAL J 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 245 through 252 removed outlier: 6.429A pdb=" N CYS J 247 " --> pdb=" O LYS J 186 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LYS J 186 " --> pdb=" O CYS J 247 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE J 249 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR J 292 " --> pdb=" O MET J 183 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE J 185 " --> pdb=" O THR J 292 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1779 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: 2.55 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3688 1.32 - 1.45: 4497 1.45 - 1.57: 10818 1.57 - 1.69: 0 1.69 - 1.82: 40 Bond restraints: 19043 Sorted by residual: bond pdb=" N ARG H 267 " pdb=" CA ARG H 267 " ideal model delta sigma weight residual 1.455 1.504 -0.049 9.60e-03 1.09e+04 2.64e+01 bond pdb=" C ALA D 195 " pdb=" N PRO D 196 " ideal model delta sigma weight residual 1.332 1.392 -0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" N PRO D 196 " pdb=" CD PRO D 196 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" CA ARG H 267 " pdb=" C ARG H 267 " ideal model delta sigma weight residual 1.519 1.565 -0.046 1.09e-02 8.42e+03 1.75e+01 bond pdb=" C20 C7B D 401 " pdb=" O06 C7B D 401 " ideal model delta sigma weight residual 1.347 1.428 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 19038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 25159 2.75 - 5.50: 1121 5.50 - 8.26: 127 8.26 - 11.01: 30 11.01 - 13.76: 11 Bond angle restraints: 26448 Sorted by residual: angle pdb=" N GLY D 200 " pdb=" CA GLY D 200 " pdb=" C GLY D 200 " ideal model delta sigma weight residual 112.73 124.79 -12.06 1.20e+00 6.94e-01 1.01e+02 angle pdb=" N HIS C 201 " pdb=" CA HIS C 201 " pdb=" C HIS C 201 " ideal model delta sigma weight residual 111.07 121.80 -10.73 1.07e+00 8.73e-01 1.01e+02 angle pdb=" N SER A 22 " pdb=" CA SER A 22 " pdb=" C SER A 22 " ideal model delta sigma weight residual 111.28 101.17 10.11 1.09e+00 8.42e-01 8.61e+01 angle pdb=" C ARG G 267 " pdb=" N PRO G 268 " pdb=" CA PRO G 268 " ideal model delta sigma weight residual 119.93 110.31 9.62 1.07e+00 8.73e-01 8.09e+01 angle pdb=" N SER J 301 " pdb=" CA SER J 301 " pdb=" C SER J 301 " ideal model delta sigma weight residual 111.14 120.16 -9.02 1.08e+00 8.57e-01 6.98e+01 ... (remaining 26443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 10939 29.56 - 59.11: 72 59.11 - 88.67: 5 88.67 - 118.22: 0 118.22 - 147.78: 1 Dihedral angle restraints: 11017 sinusoidal: 1254 harmonic: 9763 Sorted by residual: dihedral pdb=" N ARG E 384 " pdb=" C ARG E 384 " pdb=" CA ARG E 384 " pdb=" CB ARG E 384 " ideal model delta harmonic sigma weight residual 122.80 139.47 -16.67 0 2.50e+00 1.60e-01 4.44e+01 dihedral pdb=" CA ALA G 421 " pdb=" C ALA G 421 " pdb=" N GLN G 422 " pdb=" CA GLN G 422 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ALA A 129 " pdb=" C ALA A 129 " pdb=" N TYR A 130 " pdb=" CA TYR A 130 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 11014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2974 0.137 - 0.273: 341 0.273 - 0.410: 35 0.410 - 0.547: 2 0.547 - 0.683: 1 Chirality restraints: 3353 Sorted by residual: chirality pdb=" CA ARG E 384 " pdb=" N ARG E 384 " pdb=" C ARG E 384 " pdb=" CB ARG E 384 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CA ARG J 299 " pdb=" N ARG J 299 " pdb=" C ARG J 299 " pdb=" CB ARG J 299 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA THR C 253 " pdb=" N THR C 253 " pdb=" C THR C 253 " pdb=" CB THR C 253 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.37e+00 ... (remaining 3350 not shown) Planarity restraints: 3679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C09 C7B D 401 " 0.100 2.00e-02 2.50e+03 8.37e-02 8.75e+01 pdb=" C15 C7B D 401 " -0.025 2.00e-02 2.50e+03 pdb=" C17 C7B D 401 " 0.074 2.00e-02 2.50e+03 pdb=" N07 C7B D 401 " -0.137 2.00e-02 2.50e+03 pdb=" O03 C7B D 401 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 C7B D 401 " -0.048 2.00e-02 2.50e+03 4.02e-02 2.02e+01 pdb=" C16 C7B D 401 " -0.000 2.00e-02 2.50e+03 pdb=" C18 C7B D 401 " -0.032 2.00e-02 2.50e+03 pdb=" N08 C7B D 401 " 0.068 2.00e-02 2.50e+03 pdb=" O04 C7B D 401 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 266 " 0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C CYS H 266 " -0.064 2.00e-02 2.50e+03 pdb=" O CYS H 266 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG H 267 " 0.021 2.00e-02 2.50e+03 ... (remaining 3676 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 10 2.24 - 2.90: 8064 2.90 - 3.57: 24463 3.57 - 4.23: 33758 4.23 - 4.90: 54573 Nonbonded interactions: 120868 Sorted by model distance: nonbonded pdb=" O LEU G 473 " pdb=" CD1 TRP G 476 " model vdw 1.569 3.260 nonbonded pdb=" O ALA C 195 " pdb=" O PHE C 197 " model vdw 1.918 3.040 nonbonded pdb=" O HIS G 274 " pdb=" N ILE G 277 " model vdw 1.938 3.120 nonbonded pdb=" O HIS G 274 " pdb=" N ALA G 276 " model vdw 1.997 3.120 nonbonded pdb=" O LEU G 192 " pdb=" N PHE G 195 " model vdw 2.088 3.120 ... (remaining 120863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 129 or (resid 130 and (name N or name CA or name \ C or name O or name CB )) or resid 131 through 155 or (resid 156 and (name N or \ name CA or name C or name O or name CB )) or resid 157 through 271 or (resid 27 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 273 through \ 305)) selection = (chain 'B' and (resid 6 through 118 or (resid 119 through 121 and (name N or nam \ e CA or name C or name O or name CB )) or resid 122 through 148 or (resid 149 an \ d (name N or name CA or name C or name O or name CB )) or resid 150 through 158 \ or (resid 159 through 160 and (name N or name CA or name C or name O or name CB \ )) or resid 161 through 168 or (resid 169 through 172 and (name N or name CA or \ name C or name O or name CB )) or resid 173 through 177 or (resid 178 and (name \ N or name CA or name C or name O or name CB )) or resid 179 through 216 or (resi \ d 217 and (name N or name CA or name C or name O or name CB )) or resid 218 thro \ ugh 232 or (resid 233 through 234 and (name N or name CA or name C or name O or \ name CB )) or resid 235 through 305)) } ncs_group { reference = (chain 'C' and (resid 12 through 83 or (resid 84 through 92 and (name N or name \ CA or name C or name O or name CB )) or resid 93 through 153 or (resid 154 throu \ gh 157 and (name N or name CA or name C or name O or name CB )) or resid 158 thr \ ough 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) \ or resid 169 through 172 or (resid 173 through 176 and (name N or name CA or nam \ e C or name O or name CB )) or resid 177 through 178 or (resid 179 through 186 a \ nd (name N or name CA or name C or name O or name CB )) or resid 187 through 193 \ or (resid 194 through 195 and (name N or name CA or name C or name O or name CB \ )) or resid 196 through 202 or (resid 203 through 207 and (name N or name CA or \ name C or name O or name CB )) or resid 208 through 212 or (resid 213 and (name \ N or name CA or name C or name O or name CB )) or resid 214 through 217 or (res \ id 218 through 221 and (name N or name CA or name C or name O or name CB )) or r \ esid 222 through 225 or (resid 226 through 227 and (name N or name CA or name C \ or name O or name CB )) or resid 228 through 229 or (resid 230 and (name N or na \ me CA or name C or name O or name CB )) or resid 231 through 237 or (resid 238 t \ hrough 239 and (name N or name CA or name C or name O or name CB )) or resid 240 \ through 245 or (resid 246 through 249 and (name N or name CA or name C or name \ O or name CB )) or resid 250 or (resid 251 and (name N or name CA or name C or n \ ame O or name CB )) or resid 252 or (resid 253 and (name N or name CA or name C \ or name O or name CB )) or resid 254 through 255 or (resid 256 through 259 and ( \ name N or name CA or name C or name O or name CB )) or resid 260 through 261 or \ (resid 262 through 263 and (name N or name CA or name C or name O or name CB )) \ or resid 264 through 266 or (resid 267 through 269 and (name N or name CA or nam \ e C or name O or name CB )) or resid 270 through 287 or (resid 288 through 290 a \ nd (name N or name CA or name C or name O or name CB )) or resid 291 through 349 \ )) selection = (chain 'D' and (resid 12 through 82 or (resid 83 through 92 and (name N or name \ CA or name C or name O or name CB )) or resid 93 through 96 or (resid 128 throug \ h 157 and (name N or name CA or name C or name O or name CB )) or resid 158 thro \ ugh 205 or (resid 206 through 207 and (name N or name CA or name C or name O or \ name CB )) or resid 208 through 272 or (resid 273 through 275 and (name N or nam \ e CA or name C or name O or name CB )) or resid 276 through 293 or (resid 294 an \ d (name N or name CA or name C or name CB )) or (resid 295 and (name N or name C \ A or name C or name O or name CB )) or resid 296 through 307 or (resid 308 and ( \ name N or name CA or name C or name O or name CB )) or resid 309 or (resid 310 a \ nd (name N or name CA or name C or name O or name CB )) or resid 311 through 319 \ or (resid 320 through 323 and (name N or name CA or name C or name O or name CB \ )) or resid 324 or (resid 325 through 328 and (name N or name CA or name C or n \ ame O or name CB )) or resid 329 through 349)) } ncs_group { reference = (chain 'E' and (resid 1 through 66 or (resid 67 through 72 and (name N or name C \ A or name C or name O or name CB )) or resid 73 through 161 or (resid 162 throug \ h 163 and (name N or name CA or name C or name O or name CB )) or resid 164 thro \ ugh 444)) selection = (chain 'F' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ C or name CB )) or resid 162 through 444)) } ncs_group { reference = (chain 'G' and (resid 166 through 268 or (resid 269 through 273 and (name N or n \ ame CA or name C or name O or name CB )) or resid 274 through 343 or (resid 344 \ through 349 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 0 through 405 or (resid 406 through 411 and (name N or name CA or name C or name \ O or name CB )) or resid 412 through 481 or (resid 482 through 488 and (name N \ or name CA or name C or name O or name CB )) or resid 489 through 518)) selection = (chain 'H' and (resid 166 through 239 or (resid 240 through 242 and (name N or n \ ame CA or name C or name O or name CB )) or resid 243 through 518)) } ncs_group { reference = (chain 'I' and (resid 40 through 168 or (resid 169 through 189 and (name N or na \ me CA or name C or name O or name CB )) or resid 190 through 194 or (resid 195 t \ hrough 215 and (name N or name CA or name C or name O or name CB )) or resid 216 \ through 241 or (resid 242 through 259 and (name N or name CA or name C or name \ O or name CB )) or resid 260 through 288 or (resid 289 through 295 and (name N o \ r name CA or name C or name O or name CB )) or resid 296 through 311 or (resid 3 \ 12 through 316 and (name N or name CA or name C or name O or name CB )) or resid \ 317 through 342 or (resid 343 through 344 and (name N or name CA or name C or n \ ame O or name CB )) or resid 345 or (resid 346 through 350 and (name N or name C \ A or name C or name O or name CB )) or resid 351 through 450)) selection = (chain 'J' and (resid 40 through 214 or (resid 215 and (name N or name CA or nam \ e C or name O or name CB )) or resid 216 through 450)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.550 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 19043 Z= 0.535 Angle : 1.362 13.759 26448 Z= 0.894 Chirality : 0.092 0.683 3353 Planarity : 0.009 0.092 3679 Dihedral : 10.349 147.778 4651 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.75 % Allowed : 18.46 % Favored : 80.78 % Rotamer: Outliers : 3.41 % Allowed : 7.17 % Favored : 89.43 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.42 (0.12), residues: 3315 helix: -3.47 (0.11), residues: 963 sheet: -3.58 (0.21), residues: 424 loop : -3.83 (0.12), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 84 TYR 0.028 0.003 TYR H 393 PHE 0.024 0.003 PHE C 170 TRP 0.021 0.003 TRP H 476 HIS 0.011 0.003 HIS G 430 Details of bonding type rmsd covalent geometry : bond 0.00774 (19043) covalent geometry : angle 1.36234 (26448) hydrogen bonds : bond 0.18873 ( 649) hydrogen bonds : angle 11.34680 ( 1779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.666 Fit side-chains REVERT: A 137 VAL cc_start: 0.8865 (p) cc_final: 0.8595 (m) REVERT: A 272 TRP cc_start: 0.5866 (m-10) cc_final: 0.5623 (m100) REVERT: B 137 VAL cc_start: 0.8825 (p) cc_final: 0.8558 (m) REVERT: C 18 PHE cc_start: 0.8314 (t80) cc_final: 0.8103 (t80) REVERT: C 168 ILE cc_start: 0.8450 (tt) cc_final: 0.8243 (tt) REVERT: D 340 MET cc_start: 0.8602 (ttp) cc_final: 0.7530 (tmm) REVERT: E 94 TYR cc_start: 0.7824 (t80) cc_final: 0.7541 (t80) REVERT: F 94 TYR cc_start: 0.7858 (t80) cc_final: 0.7582 (t80) REVERT: H 196 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8542 (mmm) outliers start: 19 outliers final: 12 residues processed: 182 average time/residue: 0.1105 time to fit residues: 33.2421 Evaluate side-chains 139 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0030 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS F 203 HIS G 182 HIS G 479 HIS H 477 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.119555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.101962 restraints weight = 43414.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.100743 restraints weight = 68572.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101563 restraints weight = 76421.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101349 restraints weight = 48763.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.101634 restraints weight = 45216.010| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19043 Z= 0.128 Angle : 0.653 11.174 26448 Z= 0.362 Chirality : 0.048 0.161 3353 Planarity : 0.005 0.061 3679 Dihedral : 7.244 161.569 3438 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.31 % Favored : 88.54 % Rotamer: Outliers : 0.18 % Allowed : 3.41 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.42 (0.13), residues: 3315 helix: -1.81 (0.15), residues: 975 sheet: -3.15 (0.23), residues: 377 loop : -3.68 (0.12), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 370 TYR 0.010 0.001 TYR A 130 PHE 0.022 0.002 PHE D 197 TRP 0.011 0.002 TRP F 37 HIS 0.009 0.001 HIS G 479 Details of bonding type rmsd covalent geometry : bond 0.00253 (19043) covalent geometry : angle 0.65291 (26448) hydrogen bonds : bond 0.03926 ( 649) hydrogen bonds : angle 5.66691 ( 1779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.717 Fit side-chains REVERT: A 135 LEU cc_start: 0.8944 (mt) cc_final: 0.8626 (mm) REVERT: A 137 VAL cc_start: 0.8808 (p) cc_final: 0.8453 (m) REVERT: A 291 LEU cc_start: 0.9392 (tp) cc_final: 0.9037 (mt) REVERT: B 137 VAL cc_start: 0.8830 (p) cc_final: 0.8484 (m) REVERT: C 18 PHE cc_start: 0.8065 (t80) cc_final: 0.7786 (t80) REVERT: C 246 ARG cc_start: 0.6965 (ttp-170) cc_final: 0.6661 (ttm170) REVERT: E 94 TYR cc_start: 0.8060 (t80) cc_final: 0.7857 (t80) REVERT: F 94 TYR cc_start: 0.8108 (t80) cc_final: 0.7901 (t80) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.0983 time to fit residues: 27.8929 Evaluate side-chains 132 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 273 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 92 optimal weight: 0.0030 chunk 141 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 296 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.121033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.106317 restraints weight = 43972.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106104 restraints weight = 85016.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.106348 restraints weight = 79770.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106305 restraints weight = 49494.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.106561 restraints weight = 48185.546| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19043 Z= 0.129 Angle : 0.615 10.194 26448 Z= 0.338 Chirality : 0.047 0.169 3353 Planarity : 0.005 0.059 3679 Dihedral : 6.471 152.350 3438 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.60 % Favored : 85.34 % Rotamer: Outliers : 0.18 % Allowed : 3.76 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.76 (0.14), residues: 3315 helix: -0.87 (0.16), residues: 987 sheet: -3.05 (0.23), residues: 381 loop : -3.45 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 370 TYR 0.012 0.001 TYR B 9 PHE 0.019 0.002 PHE H 180 TRP 0.014 0.001 TRP H 476 HIS 0.009 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00262 (19043) covalent geometry : angle 0.61465 (26448) hydrogen bonds : bond 0.03338 ( 649) hydrogen bonds : angle 4.70822 ( 1779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.624 Fit side-chains REVERT: A 291 LEU cc_start: 0.9340 (tp) cc_final: 0.8942 (mt) REVERT: E 94 TYR cc_start: 0.7997 (t80) cc_final: 0.7789 (t80) REVERT: F 94 TYR cc_start: 0.8041 (t80) cc_final: 0.7824 (t80) REVERT: G 274 HIS cc_start: 0.7058 (p-80) cc_final: 0.6852 (p-80) REVERT: G 385 TYR cc_start: 0.7762 (t80) cc_final: 0.7512 (t80) REVERT: G 476 TRP cc_start: 0.7932 (p-90) cc_final: 0.7639 (p-90) outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.0976 time to fit residues: 27.4692 Evaluate side-chains 133 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 155 optimal weight: 40.0000 chunk 114 optimal weight: 3.9990 chunk 317 optimal weight: 0.9990 chunk 307 optimal weight: 0.9980 chunk 245 optimal weight: 0.1980 chunk 176 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.122526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.107821 restraints weight = 43639.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.107064 restraints weight = 80681.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107604 restraints weight = 83785.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.107246 restraints weight = 56035.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107556 restraints weight = 54602.157| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19043 Z= 0.107 Angle : 0.582 9.951 26448 Z= 0.314 Chirality : 0.046 0.166 3353 Planarity : 0.004 0.059 3679 Dihedral : 5.837 134.707 3438 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.67 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.30 (0.14), residues: 3315 helix: -0.28 (0.17), residues: 1003 sheet: -2.81 (0.24), residues: 398 loop : -3.29 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 84 TYR 0.014 0.001 TYR B 9 PHE 0.018 0.002 PHE C 285 TRP 0.013 0.001 TRP H 476 HIS 0.007 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00223 (19043) covalent geometry : angle 0.58171 (26448) hydrogen bonds : bond 0.02783 ( 649) hydrogen bonds : angle 4.07928 ( 1779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.685 Fit side-chains REVERT: A 291 LEU cc_start: 0.9397 (tp) cc_final: 0.9018 (mt) REVERT: D 166 MET cc_start: 0.8729 (ttp) cc_final: 0.8505 (ttm) REVERT: F 94 TYR cc_start: 0.7979 (t80) cc_final: 0.7752 (t80) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0945 time to fit residues: 26.0231 Evaluate side-chains 128 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 167 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 148 optimal weight: 40.0000 chunk 53 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 chunk 209 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 259 optimal weight: 0.7980 chunk 214 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105498 restraints weight = 43280.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.103276 restraints weight = 81471.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104025 restraints weight = 75450.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104215 restraints weight = 49808.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104505 restraints weight = 42728.208| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19043 Z= 0.117 Angle : 0.582 9.611 26448 Z= 0.314 Chirality : 0.047 0.165 3353 Planarity : 0.004 0.059 3679 Dihedral : 5.546 120.865 3438 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.36 % Favored : 86.58 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.15), residues: 3315 helix: 0.07 (0.18), residues: 1005 sheet: -2.75 (0.24), residues: 397 loop : -3.20 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 84 TYR 0.017 0.001 TYR H 240 PHE 0.018 0.002 PHE B 233 TRP 0.016 0.001 TRP G 476 HIS 0.009 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00246 (19043) covalent geometry : angle 0.58164 (26448) hydrogen bonds : bond 0.02804 ( 649) hydrogen bonds : angle 3.84464 ( 1779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.591 Fit side-chains REVERT: A 291 LEU cc_start: 0.9365 (tp) cc_final: 0.8998 (mt) REVERT: D 18 PHE cc_start: 0.8229 (t80) cc_final: 0.7887 (t80) REVERT: D 166 MET cc_start: 0.8828 (ttp) cc_final: 0.8526 (ttm) REVERT: D 340 MET cc_start: 0.7568 (ttp) cc_final: 0.7368 (ttp) REVERT: F 94 TYR cc_start: 0.8562 (t80) cc_final: 0.8344 (t80) REVERT: G 274 HIS cc_start: 0.7638 (p-80) cc_final: 0.6904 (p-80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0947 time to fit residues: 25.3360 Evaluate side-chains 130 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 289 optimal weight: 9.9990 chunk 258 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 0.0050 chunk 47 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 307 optimal weight: 0.0670 chunk 189 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 214 optimal weight: 7.9990 overall best weight: 0.3532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108623 restraints weight = 42900.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106806 restraints weight = 70661.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107587 restraints weight = 71105.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107369 restraints weight = 49941.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107656 restraints weight = 44024.076| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19043 Z= 0.089 Angle : 0.543 9.240 26448 Z= 0.288 Chirality : 0.046 0.152 3353 Planarity : 0.004 0.057 3679 Dihedral : 4.981 110.859 3438 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.02 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.15), residues: 3315 helix: 0.34 (0.18), residues: 1018 sheet: -2.50 (0.25), residues: 383 loop : -3.07 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 84 TYR 0.010 0.001 TYR B 9 PHE 0.015 0.001 PHE H 180 TRP 0.012 0.001 TRP I 317 HIS 0.008 0.001 HIS G 479 Details of bonding type rmsd covalent geometry : bond 0.00185 (19043) covalent geometry : angle 0.54350 (26448) hydrogen bonds : bond 0.02270 ( 649) hydrogen bonds : angle 3.46343 ( 1779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.576 Fit side-chains REVERT: A 291 LEU cc_start: 0.9416 (tp) cc_final: 0.8677 (mt) REVERT: C 166 MET cc_start: 0.9160 (ttp) cc_final: 0.8865 (ttm) REVERT: D 18 PHE cc_start: 0.8141 (t80) cc_final: 0.7804 (t80) REVERT: D 166 MET cc_start: 0.8654 (ttp) cc_final: 0.8312 (ttm) REVERT: F 94 TYR cc_start: 0.8516 (t80) cc_final: 0.8297 (t80) REVERT: G 274 HIS cc_start: 0.7262 (p-80) cc_final: 0.6639 (p-80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0938 time to fit residues: 26.1273 Evaluate side-chains 131 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 162 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 187 optimal weight: 0.0000 chunk 270 optimal weight: 9.9990 chunk 203 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 200 optimal weight: 0.3980 chunk 172 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS G 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.123857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107237 restraints weight = 43402.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105212 restraints weight = 76665.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.105837 restraints weight = 74132.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106071 restraints weight = 48752.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106215 restraints weight = 42868.189| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19043 Z= 0.103 Angle : 0.554 9.136 26448 Z= 0.294 Chirality : 0.046 0.161 3353 Planarity : 0.004 0.059 3679 Dihedral : 4.920 102.261 3438 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.58 % Favored : 88.36 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.15), residues: 3315 helix: 0.49 (0.18), residues: 1016 sheet: -2.48 (0.25), residues: 380 loop : -3.00 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 84 TYR 0.009 0.001 TYR H 393 PHE 0.017 0.001 PHE H 180 TRP 0.005 0.001 TRP I 317 HIS 0.007 0.001 HIS G 479 Details of bonding type rmsd covalent geometry : bond 0.00219 (19043) covalent geometry : angle 0.55416 (26448) hydrogen bonds : bond 0.02415 ( 649) hydrogen bonds : angle 3.39806 ( 1779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.753 Fit side-chains REVERT: A 291 LEU cc_start: 0.9340 (tp) cc_final: 0.8853 (mt) REVERT: C 166 MET cc_start: 0.9245 (ttp) cc_final: 0.8971 (ttm) REVERT: D 166 MET cc_start: 0.8785 (ttp) cc_final: 0.8413 (ttm) REVERT: F 94 TYR cc_start: 0.8523 (t80) cc_final: 0.8274 (t80) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0936 time to fit residues: 25.6450 Evaluate side-chains 130 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 321 optimal weight: 0.2980 chunk 313 optimal weight: 10.0000 chunk 12 optimal weight: 0.0050 chunk 269 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 0.2980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.124683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107958 restraints weight = 43050.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106028 restraints weight = 76010.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.106696 restraints weight = 73091.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.106899 restraints weight = 49336.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.107064 restraints weight = 42800.339| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19043 Z= 0.095 Angle : 0.550 9.402 26448 Z= 0.289 Chirality : 0.046 0.154 3353 Planarity : 0.004 0.057 3679 Dihedral : 4.789 98.484 3438 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.50 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.15), residues: 3315 helix: 0.56 (0.18), residues: 1027 sheet: -2.30 (0.26), residues: 373 loop : -2.95 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 84 TYR 0.007 0.001 TYR H 393 PHE 0.017 0.001 PHE H 180 TRP 0.007 0.001 TRP I 317 HIS 0.007 0.001 HIS G 479 Details of bonding type rmsd covalent geometry : bond 0.00202 (19043) covalent geometry : angle 0.54996 (26448) hydrogen bonds : bond 0.02243 ( 649) hydrogen bonds : angle 3.28594 ( 1779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.759 Fit side-chains REVERT: A 291 LEU cc_start: 0.9335 (tp) cc_final: 0.8859 (mt) REVERT: C 166 MET cc_start: 0.9164 (ttp) cc_final: 0.8906 (ttm) REVERT: D 166 MET cc_start: 0.8785 (ttp) cc_final: 0.8410 (ttm) REVERT: F 94 TYR cc_start: 0.8515 (t80) cc_final: 0.8269 (t80) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0937 time to fit residues: 25.9212 Evaluate side-chains 129 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 23 optimal weight: 5.9990 chunk 186 optimal weight: 0.0010 chunk 111 optimal weight: 2.9990 chunk 296 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 133 optimal weight: 0.0770 overall best weight: 1.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS G 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.106203 restraints weight = 43498.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105479 restraints weight = 90386.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105820 restraints weight = 89867.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105820 restraints weight = 52929.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106144 restraints weight = 47568.508| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19043 Z= 0.160 Angle : 0.619 9.549 26448 Z= 0.332 Chirality : 0.048 0.165 3353 Planarity : 0.004 0.059 3679 Dihedral : 5.353 93.589 3438 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.29 % Favored : 84.65 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.15), residues: 3315 helix: 0.51 (0.18), residues: 1011 sheet: -2.52 (0.25), residues: 392 loop : -3.03 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 84 TYR 0.016 0.002 TYR J 296 PHE 0.020 0.002 PHE D 285 TRP 0.015 0.002 TRP G 476 HIS 0.006 0.002 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00336 (19043) covalent geometry : angle 0.61871 (26448) hydrogen bonds : bond 0.02961 ( 649) hydrogen bonds : angle 3.72025 ( 1779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.744 Fit side-chains REVERT: A 291 LEU cc_start: 0.9280 (tp) cc_final: 0.8598 (mt) REVERT: D 166 MET cc_start: 0.8854 (ttp) cc_final: 0.8565 (ttm) REVERT: F 94 TYR cc_start: 0.8498 (t80) cc_final: 0.8239 (t80) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0881 time to fit residues: 23.6395 Evaluate side-chains 126 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 65 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 296 optimal weight: 10.0000 chunk 229 optimal weight: 0.0010 chunk 136 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 overall best weight: 2.7592 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.118448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103281 restraints weight = 44137.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102349 restraints weight = 96773.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.102947 restraints weight = 93687.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103048 restraints weight = 55688.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103326 restraints weight = 52874.155| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19043 Z= 0.233 Angle : 0.711 10.682 26448 Z= 0.388 Chirality : 0.050 0.173 3353 Planarity : 0.005 0.061 3679 Dihedral : 6.214 93.935 3438 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 17.13 % Favored : 82.78 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.15), residues: 3315 helix: 0.16 (0.18), residues: 982 sheet: -2.70 (0.25), residues: 399 loop : -3.21 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 246 TYR 0.024 0.002 TYR J 296 PHE 0.028 0.003 PHE D 285 TRP 0.012 0.002 TRP H 366 HIS 0.016 0.002 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00488 (19043) covalent geometry : angle 0.71094 (26448) hydrogen bonds : bond 0.03630 ( 649) hydrogen bonds : angle 4.36569 ( 1779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.629 Fit side-chains REVERT: A 137 VAL cc_start: 0.8838 (p) cc_final: 0.8586 (m) REVERT: F 94 TYR cc_start: 0.8479 (t80) cc_final: 0.8222 (t80) REVERT: I 343 TYR cc_start: 0.7475 (m-10) cc_final: 0.6802 (m-80) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0910 time to fit residues: 24.5096 Evaluate side-chains 132 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 147 optimal weight: 40.0000 chunk 178 optimal weight: 20.0000 chunk 282 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 223 optimal weight: 1.9990 chunk 262 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.121050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105869 restraints weight = 43671.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105090 restraints weight = 88225.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105406 restraints weight = 90152.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105465 restraints weight = 54377.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105762 restraints weight = 49059.061| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19043 Z= 0.132 Angle : 0.611 10.561 26448 Z= 0.326 Chirality : 0.047 0.157 3353 Planarity : 0.004 0.058 3679 Dihedral : 5.599 100.349 3438 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.60 % Favored : 86.30 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.15), residues: 3315 helix: 0.50 (0.18), residues: 997 sheet: -2.51 (0.26), residues: 368 loop : -3.15 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 84 TYR 0.015 0.001 TYR H 307 PHE 0.022 0.002 PHE D 285 TRP 0.027 0.002 TRP H 366 HIS 0.006 0.001 HIS G 479 Details of bonding type rmsd covalent geometry : bond 0.00281 (19043) covalent geometry : angle 0.61058 (26448) hydrogen bonds : bond 0.02751 ( 649) hydrogen bonds : angle 3.83114 ( 1779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2117.77 seconds wall clock time: 37 minutes 3.38 seconds (2223.38 seconds total)