Starting phenix.real_space_refine on Wed Mar 4 17:26:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mlv_23911/03_2026/7mlv_23911.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mlv_23911/03_2026/7mlv_23911.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/7mlv_23911/03_2026/7mlv_23911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mlv_23911/03_2026/7mlv_23911.map" model { file = "/net/cci-nas-00/data/ceres_data/7mlv_23911/03_2026/7mlv_23911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mlv_23911/03_2026/7mlv_23911.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= 0.003 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 9653 2.51 5 N 2448 2.21 5 O 2860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15055 Number of models: 1 Model: "" Number of chains: 16 Chain: "J" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 782 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 878 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 777 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 884 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 777 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 875 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1299 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain breaks: 4 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 4, 'ASP:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2456 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 14, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2292 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 14, 'TRANS': 281} Chain breaks: 4 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 4, 'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2125 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 68 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.47, per 1000 atoms: 0.23 Number of scatterers: 15055 At special positions: 0 Unit cell: (154.462, 131.334, 118.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 94 16.00 O 2860 8.00 N 2448 7.00 C 9653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM14862 O5 NAG O 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 501 " - " MAN D 502 " " MAN P 5 " - " MAN P 6 " ALPHA1-3 " MAN D 501 " - " BMA D 503 " ~> Even though BMA is a beta isomer, an alpha linkage is required... " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA D 503 " - " MAN D 507 " " MAN D 504 " - " MAN D 507 " " BMA N 3 " - " MAN N 5 " " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 5 " BETA1-4 " BMA D 503 " - " NAG D 506 " " NAG D 505 " - " NAG D 506 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG N 1 " - " ASN A 38 " " NAG O 1 " - " ASN B 38 " " NAG P 1 " - " ASN C 38 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 562.7 milliseconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3558 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 38 sheets defined 14.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.956A pdb=" N LYS F 65 " --> pdb=" O GLU F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.813A pdb=" N ASP L 90 " --> pdb=" O THR L 87 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER L 91 " --> pdb=" O SER L 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 87 through 91' Processing helix chain 'D' and resid 10 through 16 removed outlier: 4.333A pdb=" N PHE D 13 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 14 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP D 15 " --> pdb=" O ASP D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.521A pdb=" N ALA D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 4.047A pdb=" N SER D 92 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 93' Processing helix chain 'D' and resid 162 through 166 removed outlier: 4.001A pdb=" N ASP D 165 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.516A pdb=" N MET A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.830A pdb=" N VAL A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.602A pdb=" N LEU A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.850A pdb=" N SER A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 removed outlier: 4.375A pdb=" N ALA A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N CYS A 290 " --> pdb=" O TRP A 286 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 406 through 417 removed outlier: 4.071A pdb=" N PHE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 18 removed outlier: 3.838A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.862A pdb=" N MET B 89 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.966A pdb=" N ILE B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.714A pdb=" N ILE B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 281 through 282 No H-bonds generated for 'chain 'B' and resid 281 through 282' Processing helix chain 'B' and resid 284 through 284 No H-bonds generated for 'chain 'B' and resid 284 through 284' Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.633A pdb=" N PHE B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 403 through 417 removed outlier: 3.621A pdb=" N LEU B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.651A pdb=" N LEU C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 74' Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.943A pdb=" N SER C 92 " --> pdb=" O MET C 89 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 93' Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.760A pdb=" N SER C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.895A pdb=" N GLY C 269 " --> pdb=" O THR C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 297 removed outlier: 3.680A pdb=" N LEU C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 406 Proline residue: C 403 - end of helix Processing helix chain 'C' and resid 406 through 417 removed outlier: 4.057A pdb=" N MET C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 412 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.715A pdb=" N THR J 5 " --> pdb=" O LYS J 24 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS J 23 " --> pdb=" O TYR J 71 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.504A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN J 37 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR J 36 " --> pdb=" O TYR J 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 62 through 63 removed outlier: 4.266A pdb=" N THR J 63 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR J 74 " --> pdb=" O THR J 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'G' and resid 19 through 21 removed outlier: 3.823A pdb=" N ILE G 20 " --> pdb=" O MET G 81 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET G 81 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR G 78 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 58 through 60 removed outlier: 3.858A pdb=" N ASN G 59 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU G 50 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP G 47 " --> pdb=" O LYS G 38 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 92 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU G 114 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 36 through 37 Processing sheet with id=AA8, first strand: chain 'K' and resid 65 through 67 Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.782A pdb=" N GLU F 10 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN F 39 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR F 95 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU F 37 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 34 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 51 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TRP F 36 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU F 50 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN F 59 " --> pdb=" O GLU F 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.950A pdb=" N ILE F 20 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET F 81 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR F 78 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.987A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR M 49 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 62 through 67 removed outlier: 3.715A pdb=" N THR M 72 " --> pdb=" O SER M 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'L' and resid 46 through 51 removed outlier: 6.201A pdb=" N TRP L 47 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP L 36 " --> pdb=" O GLY L 49 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE L 51 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE L 34 " --> pdb=" O ILE L 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 68 through 73 removed outlier: 4.037A pdb=" N THR L 71 " --> pdb=" O TYR L 80 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU L 73 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR L 78 " --> pdb=" O GLU L 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.640A pdb=" N GLN I 37 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AC2, first strand: chain 'I' and resid 63 through 66 Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.822A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.983A pdb=" N ILE H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR H 78 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.611A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE H 51 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR H 95 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU H 114 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR H 94 " --> pdb=" O THR H 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 39 through 41 removed outlier: 5.872A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 61 through 68 removed outlier: 3.616A pdb=" N ILE D 132 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 64 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 120 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 83 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 195 through 196 removed outlier: 3.881A pdb=" N ARG D 196 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 211 " --> pdb=" O ARG D 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 37 through 38 removed outlier: 5.912A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 60 through 69 removed outlier: 3.527A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.944A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.732A pdb=" N CYS A 152 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 214 " --> pdb=" O CYS A 152 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.722A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 125 through 137 removed outlier: 3.721A pdb=" N ILE B 130 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 62 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 134 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 60 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 177 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE B 45 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.076A pdb=" N LEU B 83 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 118 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 150 through 155 removed outlier: 3.636A pdb=" N CYS B 152 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 154 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 212 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 217 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 131 through 132 removed outlier: 7.226A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 46 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 169 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.877A pdb=" N PHE C 99 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU C 157 " --> pdb=" O PHE C 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 149 through 152 removed outlier: 3.513A pdb=" N CYS C 152 " --> pdb=" O PHE C 214 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 200 through 201 258 hydrogen bonds defined for protein. 648 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: 2.20 Time building geometry restraints manager: 1.79 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: 2428 1.32 - 1.45: 4559 1.45 - 1.58: 8276 1.58 - 1.71: 1 1.71 - 1.84: 150 Bond restraints: 15414 Sorted by residual: bond pdb=" CA LEU D 64 " pdb=" C LEU D 64 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.25e-02 6.40e+03 4.60e+01 bond pdb=" CA ILE D 62 " pdb=" C ILE D 62 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.27e-02 6.20e+03 2.89e+01 bond pdb=" CA PHE D 63 " pdb=" C PHE D 63 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.34e-02 5.57e+03 2.21e+01 bond pdb=" C5 MAN D 507 " pdb=" O5 MAN D 507 " ideal model delta sigma weight residual 1.418 1.489 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C ILE C 28 " pdb=" N ARG C 29 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.07e-02 2.33e+03 1.21e+01 ... (remaining 15409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 20124 2.28 - 4.56: 645 4.56 - 6.84: 132 6.84 - 9.13: 26 9.13 - 11.41: 14 Bond angle restraints: 20941 Sorted by residual: angle pdb=" N LEU D 64 " pdb=" CA LEU D 64 " pdb=" C LEU D 64 " ideal model delta sigma weight residual 110.17 99.91 10.26 1.61e+00 3.86e-01 4.06e+01 angle pdb=" C TYR C 228 " pdb=" N ILE C 229 " pdb=" CA ILE C 229 " ideal model delta sigma weight residual 120.33 124.86 -4.53 8.00e-01 1.56e+00 3.21e+01 angle pdb=" N VAL A 253 " pdb=" CA VAL A 253 " pdb=" C VAL A 253 " ideal model delta sigma weight residual 112.90 108.16 4.74 9.60e-01 1.09e+00 2.44e+01 angle pdb=" C PRO C 185 " pdb=" N GLN C 186 " pdb=" CA GLN C 186 " ideal model delta sigma weight residual 121.54 130.92 -9.38 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C VAL K 29 " pdb=" N SER K 30 " pdb=" CA SER K 30 " ideal model delta sigma weight residual 121.19 128.90 -7.71 1.59e+00 3.96e-01 2.35e+01 ... (remaining 20936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 8891 23.49 - 46.99: 312 46.99 - 70.48: 33 70.48 - 93.97: 47 93.97 - 117.47: 34 Dihedral angle restraints: 9317 sinusoidal: 3769 harmonic: 5548 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 16.97 76.03 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 155.05 -62.05 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CA CYS C 198 " pdb=" C CYS C 198 " pdb=" N THR C 199 " pdb=" CA THR C 199 " ideal model delta harmonic sigma weight residual -180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 9314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 2388 0.164 - 0.328: 21 0.328 - 0.492: 1 0.492 - 0.657: 0 0.657 - 0.821: 1 Chirality restraints: 2411 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 38 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" C1 MAN P 4 " pdb=" O6 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 2.46 -0.06 2.00e-02 2.50e+03 9.99e+00 chirality pdb=" C1 BMA D 503 " pdb=" C2 BMA D 503 " pdb=" O5 BMA D 503 " pdb=" O4 NAG D 506 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.39e+00 ... (remaining 2408 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 38 " -0.124 2.00e-02 2.50e+03 2.45e-01 7.49e+02 pdb=" CG ASN C 38 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN C 38 " 0.249 2.00e-02 2.50e+03 pdb=" ND2 ASN C 38 " -0.364 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 38 " 0.050 2.00e-02 2.50e+03 6.46e-02 5.22e+01 pdb=" CG ASN B 38 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 38 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 38 " -0.109 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 61 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C ASN D 61 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN D 61 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE D 62 " 0.017 2.00e-02 2.50e+03 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 645 2.71 - 3.26: 13255 3.26 - 3.81: 23360 3.81 - 4.35: 28119 4.35 - 4.90: 45532 Nonbonded interactions: 110911 Sorted by model distance: nonbonded pdb=" OG SER A 40 " pdb=" O7 NAG N 1 " model vdw 2.168 3.040 nonbonded pdb=" OD1 ASN D 38 " pdb=" C1 NAG D 505 " model vdw 2.194 3.470 nonbonded pdb=" OG SER J 14 " pdb=" OD2 ASP J 17 " model vdw 2.299 3.040 nonbonded pdb=" OG SER I 14 " pdb=" OD2 ASP I 17 " model vdw 2.303 3.040 nonbonded pdb=" OD1 ASN B 38 " pdb=" C8 NAG O 1 " model vdw 2.304 3.460 ... (remaining 110906 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 10 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 24 or (resid 25 through 28 and (na \ me N or name CA or name C or name O or name CB )) or resid 29 through 32 or (res \ id 33 and (name N or name CA or name C or name O or name CB )) or resid 34 throu \ gh 41 or (resid 42 through 43 and (name N or name CA or name C or name O or name \ CB )) or resid 44 through 49 or (resid 50 and (name N or name CA or name C or n \ ame O or name CB )) or resid 58 or (resid 59 through 60 and (name N or name CA o \ r name C or name O or name CB )) or resid 61 through 64 or (resid 65 and (name N \ or name CA or name C or name O or name CB )) or resid 66 through 75 or (resid 7 \ 6 through 77 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 8 through 83 or (resid 84 and (name N or name CA or name C or name O or name CB \ )) or resid 85 or (resid 86 and (name N or name CA or name C or name O or name C \ B )) or resid 87 or (resid 88 and (name N or name CA or name C or name O or name \ CB )) or resid 89 through 90 or (resid 91 and (name N or name CA or name C or n \ ame O or name CB )) or resid 92 through 94 or (resid 95 and (name N or name CA o \ r name C or name O or name CB )) or resid 96 through 103 or resid 115 through 12 \ 1 or (resid 122 through 123 and (name N or name CA or name C or name O or name C \ B )) or resid 124 through 131 or (resid 132 and (name N or name CA or name C or \ name O or name CB )) or resid 133 through 140 or (resid 141 and (name N or name \ CA or name C or name O or name CB )) or resid 142 through 144 or (resid 145 and \ (name N or name CA or name C or name O or name CB )) or resid 146 or (resid 147 \ through 149 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 0 through 155 or (resid 156 through 157 and (name N or name CA or name C or name \ O or name CB )) or resid 158 through 171 or (resid 172 through 173 and (name N \ or name CA or name C or name O or name CB )) or resid 174 through 185 or (resid \ 186 and (name N or name CA or name C or name O or name CB )) or resid 187 throug \ h 189 or (resid 190 through 192 and (name N or name CA or name C or name O or na \ me CB )) or resid 193 through 203 or (resid 204 and (name N or name CA or name C \ or name O or name CB )) or resid 205 through 210 or (resid 211 through 213 and \ (name N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB )) or resid 216 or (resid \ 217 through 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 223 or (resid 224 through 225 and (name N or name CA or name C or \ name O or name CB )) or resid 226 through 239 or resid 255 through 273 or resid \ 282 or resid 284 through 299 or resid 399 through 419)) selection = (chain 'B' and (resid 10 through 15 or (resid 16 and (name N or name CA or name \ C or name O or name CB )) or resid 17 through 19 or (resid 20 and (name N or nam \ e CA or name C or name O or name CB )) or resid 21 through 24 or (resid 25 throu \ gh 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throu \ gh 31 or (resid 32 through 33 and (name N or name CA or name C or name O or name \ CB )) or resid 34 through 42 or (resid 43 and (name N or name CA or name C or n \ ame O or name CB )) or resid 44 through 49 or (resid 50 and (name N or name CA o \ r name C or name O or name CB )) or resid 58 or (resid 59 through 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 through 68 or (resid 6 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 70 through 7 \ 1 or (resid 72 and (name N or name CA or name C or name O or name CB )) or resid \ 73 through 115 or (resid 116 and (name N or name CA or name C or name O or name \ CB )) or resid 117 through 144 or (resid 145 and (name N or name CA or name C o \ r name O or name CB )) or resid 146 through 155 or (resid 156 through 157 and (n \ ame N or name CA or name C or name O or name CB )) or resid 158 through 171 or ( \ resid 172 through 173 and (name N or name CA or name C or name O or name CB )) o \ r resid 174 through 182 or (resid 183 and (name N or name CA or name C or name O \ or name CB )) or resid 184 through 188 or (resid 189 through 192 and (name N or \ name CA or name C or name O or name CB )) or resid 193 through 203 or (resid 20 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 205 through \ 210 or (resid 211 through 213 and (name N or name CA or name C or name O or name \ CB )) or resid 214 through 239 or resid 255 through 273 or resid 282 through 29 \ 9 or resid 399 through 419)) selection = (chain 'C' and (resid 10 through 31 or (resid 32 through 33 and (name N or name \ CA or name C or name O or name CB )) or resid 34 through 41 or (resid 42 through \ 43 and (name N or name CA or name C or name O or name CB )) or resid 44 through \ 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or res \ id 61 through 64 or (resid 65 and (name N or name CA or name C or name O or name \ CB )) or resid 66 through 68 or (resid 69 and (name N or name CA or name C or n \ ame O or name CB )) or resid 70 through 75 or (resid 76 through 77 and (name N o \ r name CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 \ and (name N or name CA or name C or name O or name CB )) or resid 85 or (resid 8 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 87 or (resid \ 88 and (name N or name CA or name C or name O or name CB )) or resid 89 through \ 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or res \ id 92 through 103 or resid 115 or (resid 116 and (name N or name CA or name C or \ name O or name CB )) or resid 117 through 121 or (resid 122 through 123 and (na \ me N or name CA or name C or name O or name CB )) or resid 124 through 131 or (r \ esid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 t \ hrough 140 or (resid 141 and (name N or name CA or name C or name O or name CB ) \ ) or resid 142 through 147 or (resid 148 through 149 and (name N or name CA or n \ ame C or name O or name CB )) or resid 150 through 156 or (resid 157 and (name N \ or name CA or name C or name O or name CB )) or resid 158 through 182 or (resid \ 183 and (name N or name CA or name C or name O or name CB )) or resid 184 throu \ gh 188 or (resid 189 through 192 and (name N or name CA or name C or name O or n \ ame CB )) or resid 193 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or n \ ame C or name O or name CB )) or resid 216 through 218 or (resid 219 through 220 \ and (name N or name CA or name C or name O or name CB )) or resid 221 through 2 \ 23 or (resid 224 through 225 and (name N or name CA or name C or name O or name \ CB )) or resid 226 through 282 or resid 284 through 299 or resid 399 through 419 \ )) } ncs_group { reference = (chain 'F' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 116)) selection = (chain 'G' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 30 or (resid 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 through 116)) selection = (chain 'H' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 116)) selection = (chain 'L' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 116)) } ncs_group { reference = (chain 'I' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 60 or (resid 61 and (name N or name CA \ or name C or name O or name CB )) or resid 62 through 102)) selection = (chain 'J' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 102)) selection = (chain 'K' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 17 or (resid 18 and (name N or name CA \ or name C or name O or name CB )) or resid 19 through 60 or (resid 61 and (name \ N or name CA or name C or name O or name CB )) or resid 62 through 91 or (resid \ 92 and (name N or name CA or name C or name O or name CB )) or resid 93 through \ 102)) selection = (chain 'M' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 17 or (resid 18 and (name N or name CA \ or name C or name O or name CB )) or resid 19 through 102)) } 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.960 Find NCS groups from input model: 0.290 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4164 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 : 0.005 0.219 15450 Z= 0.282 Angle : 1.095 30.364 21034 Z= 0.542 Chirality : 0.058 0.821 2411 Planarity : 0.007 0.068 2586 Dihedral : 15.502 117.467 5714 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.14 (0.14), residues: 1865 helix: -4.75 (0.12), residues: 227 sheet: -2.77 (0.21), residues: 494 loop : -3.60 (0.13), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 213 TYR 0.018 0.002 TYR C 58 PHE 0.022 0.002 PHE H 105 TRP 0.029 0.002 TRP I 50 HIS 0.004 0.001 HIS L 27 Details of bonding type rmsd covalent geometry : bond 0.00482 (15414) covalent geometry : angle 1.02499 (20941) SS BOND : bond 0.00446 ( 15) SS BOND : angle 2.03764 ( 30) hydrogen bonds : bond 0.32868 ( 258) hydrogen bonds : angle 12.55208 ( 648) link_ALPHA1-2 : bond 0.01043 ( 2) link_ALPHA1-2 : angle 1.68161 ( 6) link_ALPHA1-3 : bond 0.00828 ( 3) link_ALPHA1-3 : angle 1.89084 ( 9) link_ALPHA1-6 : bond 0.00715 ( 5) link_ALPHA1-6 : angle 2.43784 ( 15) link_BETA1-4 : bond 0.01014 ( 8) link_BETA1-4 : angle 3.85944 ( 24) link_NAG-ASN : bond 0.14805 ( 3) link_NAG-ASN : angle 17.02646 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 55 HIS cc_start: 0.5158 (t-90) cc_final: 0.4621 (t70) REVERT: K 3 VAL cc_start: 0.7610 (m) cc_final: 0.7007 (m) REVERT: K 4 MET cc_start: 0.2508 (mmm) cc_final: 0.2134 (tpt) REVERT: F 98 MET cc_start: 0.2150 (ttp) cc_final: 0.0932 (mtp) REVERT: I 4 MET cc_start: 0.3514 (tmm) cc_final: 0.2582 (tpt) REVERT: B 257 ILE cc_start: 0.7469 (mt) cc_final: 0.7000 (mm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1547 time to fit residues: 53.4441 Evaluate side-chains 147 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN A 46 ASN A 67 GLN A 125 ASN A 150 GLN A 171 GLN A 215 HIS B 115 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.055268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.048699 restraints weight = 215060.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.049293 restraints weight = 177138.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.049660 restraints weight = 136241.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.049805 restraints weight = 119385.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.049910 restraints weight = 108149.637| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15450 Z= 0.161 Angle : 0.736 12.564 21034 Z= 0.356 Chirality : 0.047 0.259 2411 Planarity : 0.005 0.077 2586 Dihedral : 14.246 108.119 2486 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.13 % Allowed : 4.24 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.33 (0.16), residues: 1865 helix: -3.71 (0.20), residues: 237 sheet: -2.35 (0.21), residues: 491 loop : -3.05 (0.15), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 18 TYR 0.020 0.002 TYR J 49 PHE 0.016 0.002 PHE M 10 TRP 0.019 0.002 TRP F 108 HIS 0.005 0.001 HIS J 91 Details of bonding type rmsd covalent geometry : bond 0.00352 (15414) covalent geometry : angle 0.71258 (20941) SS BOND : bond 0.00334 ( 15) SS BOND : angle 1.02041 ( 30) hydrogen bonds : bond 0.04316 ( 258) hydrogen bonds : angle 8.31913 ( 648) link_ALPHA1-2 : bond 0.01250 ( 2) link_ALPHA1-2 : angle 2.67628 ( 6) link_ALPHA1-3 : bond 0.01198 ( 3) link_ALPHA1-3 : angle 3.84919 ( 9) link_ALPHA1-6 : bond 0.00565 ( 5) link_ALPHA1-6 : angle 2.83850 ( 15) link_BETA1-4 : bond 0.01222 ( 8) link_BETA1-4 : angle 3.22987 ( 24) link_NAG-ASN : bond 0.01633 ( 3) link_NAG-ASN : angle 4.55405 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 LEU cc_start: 0.7417 (tp) cc_final: 0.6940 (tp) REVERT: K 3 VAL cc_start: 0.7981 (m) cc_final: 0.7464 (m) REVERT: K 4 MET cc_start: 0.3066 (mmm) cc_final: 0.2683 (tpt) REVERT: M 4 MET cc_start: 0.6364 (mmm) cc_final: 0.5895 (mmm) REVERT: I 4 MET cc_start: 0.3781 (tmm) cc_final: 0.2803 (tpt) REVERT: D 173 GLN cc_start: 0.7812 (pm20) cc_final: 0.7299 (pm20) REVERT: A 18 MET cc_start: 0.6126 (tmm) cc_final: 0.5916 (tmm) REVERT: B 202 TYR cc_start: 0.5863 (m-80) cc_final: 0.5604 (m-80) REVERT: B 411 MET cc_start: 0.8764 (mmp) cc_final: 0.8365 (mmm) REVERT: C 200 LYS cc_start: 0.6003 (mtmm) cc_final: 0.4813 (mtmm) outliers start: 2 outliers final: 1 residues processed: 187 average time/residue: 0.1507 time to fit residues: 39.4187 Evaluate side-chains 149 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 96 optimal weight: 0.0470 chunk 127 optimal weight: 40.0000 chunk 185 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 overall best weight: 3.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.053340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.044983 restraints weight = 203183.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.045299 restraints weight = 162664.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.045301 restraints weight = 132677.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.045304 restraints weight = 132451.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.045572 restraints weight = 132250.823| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15450 Z= 0.191 Angle : 0.759 13.537 21034 Z= 0.372 Chirality : 0.047 0.322 2411 Planarity : 0.005 0.054 2586 Dihedral : 12.952 111.966 2486 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.06 % Allowed : 5.47 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.16), residues: 1865 helix: -2.94 (0.26), residues: 239 sheet: -2.43 (0.20), residues: 546 loop : -2.70 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 96 TYR 0.020 0.002 TYR F 80 PHE 0.028 0.002 PHE B 242 TRP 0.066 0.003 TRP B 239 HIS 0.010 0.002 HIS J 55 Details of bonding type rmsd covalent geometry : bond 0.00416 (15414) covalent geometry : angle 0.74217 (20941) SS BOND : bond 0.00998 ( 15) SS BOND : angle 1.73465 ( 30) hydrogen bonds : bond 0.04106 ( 258) hydrogen bonds : angle 7.28144 ( 648) link_ALPHA1-2 : bond 0.01957 ( 2) link_ALPHA1-2 : angle 2.45244 ( 6) link_ALPHA1-3 : bond 0.01378 ( 3) link_ALPHA1-3 : angle 2.25578 ( 9) link_ALPHA1-6 : bond 0.01068 ( 5) link_ALPHA1-6 : angle 2.51358 ( 15) link_BETA1-4 : bond 0.01156 ( 8) link_BETA1-4 : angle 2.56527 ( 24) link_NAG-ASN : bond 0.01195 ( 3) link_NAG-ASN : angle 4.02700 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.6897 (mmm) cc_final: 0.6671 (mmm) REVERT: M 4 MET cc_start: 0.6726 (mmm) cc_final: 0.5716 (mmm) REVERT: L 81 MET cc_start: 0.4240 (tpt) cc_final: 0.4003 (tpt) REVERT: I 4 MET cc_start: 0.4124 (tmm) cc_final: 0.3017 (tpt) REVERT: H 69 THR cc_start: 0.8320 (p) cc_final: 0.7780 (p) REVERT: H 71 THR cc_start: 0.5903 (m) cc_final: 0.5247 (m) REVERT: D 173 GLN cc_start: 0.7991 (pm20) cc_final: 0.7683 (pm20) REVERT: A 81 ASP cc_start: 0.6229 (t0) cc_final: 0.5880 (t70) REVERT: B 404 MET cc_start: 0.9548 (ppp) cc_final: 0.9309 (ppp) REVERT: B 411 MET cc_start: 0.9062 (mmp) cc_final: 0.8604 (mmm) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1426 time to fit residues: 36.0581 Evaluate side-chains 135 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 97 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 85 optimal weight: 0.0040 chunk 146 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 86 optimal weight: 0.0070 chunk 119 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.053312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.046449 restraints weight = 208833.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.046909 restraints weight = 161177.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.047103 restraints weight = 133787.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.047369 restraints weight = 121861.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.047452 restraints weight = 111022.236| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15450 Z= 0.119 Angle : 0.688 11.482 21034 Z= 0.325 Chirality : 0.046 0.292 2411 Planarity : 0.004 0.048 2586 Dihedral : 11.791 110.378 2486 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.17), residues: 1865 helix: -2.49 (0.28), residues: 232 sheet: -2.35 (0.20), residues: 536 loop : -2.51 (0.16), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 101 TYR 0.023 0.001 TYR M 49 PHE 0.015 0.001 PHE A 99 TRP 0.020 0.001 TRP B 239 HIS 0.007 0.001 HIS J 91 Details of bonding type rmsd covalent geometry : bond 0.00257 (15414) covalent geometry : angle 0.67167 (20941) SS BOND : bond 0.00177 ( 15) SS BOND : angle 0.89041 ( 30) hydrogen bonds : bond 0.03125 ( 258) hydrogen bonds : angle 6.82466 ( 648) link_ALPHA1-2 : bond 0.02052 ( 2) link_ALPHA1-2 : angle 2.44159 ( 6) link_ALPHA1-3 : bond 0.01233 ( 3) link_ALPHA1-3 : angle 2.50060 ( 9) link_ALPHA1-6 : bond 0.00923 ( 5) link_ALPHA1-6 : angle 2.43043 ( 15) link_BETA1-4 : bond 0.00922 ( 8) link_BETA1-4 : angle 2.47073 ( 24) link_NAG-ASN : bond 0.01103 ( 3) link_NAG-ASN : angle 4.13355 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.3366 (mmm) cc_final: 0.3155 (mmm) REVERT: F 80 TYR cc_start: 0.7707 (m-80) cc_final: 0.7260 (m-80) REVERT: M 4 MET cc_start: 0.6950 (mmm) cc_final: 0.5993 (mmm) REVERT: I 4 MET cc_start: 0.4189 (tmm) cc_final: 0.3126 (tpt) REVERT: H 114 LEU cc_start: 0.8071 (mm) cc_final: 0.7229 (mm) REVERT: D 69 ASN cc_start: 0.8157 (t0) cc_final: 0.7924 (t0) REVERT: D 173 GLN cc_start: 0.8099 (pm20) cc_final: 0.7737 (pm20) REVERT: B 140 MET cc_start: 0.6287 (ttt) cc_final: 0.6052 (ttm) REVERT: B 411 MET cc_start: 0.8828 (mmp) cc_final: 0.8492 (mmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1332 time to fit residues: 31.9251 Evaluate side-chains 138 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 6 optimal weight: 0.9980 chunk 124 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 43 optimal weight: 30.0000 chunk 164 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.052158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.043647 restraints weight = 207464.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.044080 restraints weight = 164059.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.044319 restraints weight = 132690.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.044614 restraints weight = 115656.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.044707 restraints weight = 103297.374| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15450 Z= 0.158 Angle : 0.730 20.479 21034 Z= 0.344 Chirality : 0.046 0.280 2411 Planarity : 0.005 0.120 2586 Dihedral : 10.726 112.049 2486 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.17), residues: 1865 helix: -1.99 (0.31), residues: 233 sheet: -2.36 (0.21), residues: 530 loop : -2.33 (0.16), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 29 TYR 0.020 0.002 TYR A 228 PHE 0.020 0.002 PHE I 62 TRP 0.021 0.002 TRP C 94 HIS 0.013 0.002 HIS J 91 Details of bonding type rmsd covalent geometry : bond 0.00347 (15414) covalent geometry : angle 0.71502 (20941) SS BOND : bond 0.00262 ( 15) SS BOND : angle 1.25743 ( 30) hydrogen bonds : bond 0.03284 ( 258) hydrogen bonds : angle 6.63366 ( 648) link_ALPHA1-2 : bond 0.02198 ( 2) link_ALPHA1-2 : angle 2.94066 ( 6) link_ALPHA1-3 : bond 0.01142 ( 3) link_ALPHA1-3 : angle 2.31471 ( 9) link_ALPHA1-6 : bond 0.00991 ( 5) link_ALPHA1-6 : angle 2.33998 ( 15) link_BETA1-4 : bond 0.00845 ( 8) link_BETA1-4 : angle 2.34674 ( 24) link_NAG-ASN : bond 0.00856 ( 3) link_NAG-ASN : angle 4.14436 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.7711 (mmm) cc_final: 0.7219 (mmt) REVERT: F 81 MET cc_start: 0.6435 (mmm) cc_final: 0.5794 (mmm) REVERT: M 4 MET cc_start: 0.7262 (mmm) cc_final: 0.6126 (mmm) REVERT: I 4 MET cc_start: 0.4376 (tmm) cc_final: 0.3360 (tpt) REVERT: D 173 GLN cc_start: 0.8012 (pm20) cc_final: 0.7756 (pm20) REVERT: A 81 ASP cc_start: 0.6309 (t0) cc_final: 0.5999 (t0) REVERT: A 263 MET cc_start: 0.8070 (tmm) cc_final: 0.7793 (tmm) REVERT: B 140 MET cc_start: 0.6297 (ttt) cc_final: 0.6067 (ttm) REVERT: B 404 MET cc_start: 0.9569 (ppp) cc_final: 0.9301 (ppp) REVERT: B 411 MET cc_start: 0.9100 (mmp) cc_final: 0.8693 (mmm) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1339 time to fit residues: 32.5266 Evaluate side-chains 133 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 72 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 164 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 128 optimal weight: 0.0670 chunk 174 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 overall best weight: 2.8724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.051422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.042974 restraints weight = 207392.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.043335 restraints weight = 165099.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.043506 restraints weight = 132344.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.043506 restraints weight = 117067.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.043506 restraints weight = 117067.821| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15450 Z= 0.151 Angle : 0.711 15.726 21034 Z= 0.337 Chirality : 0.046 0.302 2411 Planarity : 0.004 0.048 2586 Dihedral : 10.084 112.779 2486 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.17), residues: 1865 helix: -1.81 (0.31), residues: 244 sheet: -2.39 (0.21), residues: 494 loop : -2.22 (0.16), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 119 TYR 0.021 0.002 TYR M 49 PHE 0.017 0.002 PHE K 62 TRP 0.027 0.002 TRP A 414 HIS 0.015 0.002 HIS J 91 Details of bonding type rmsd covalent geometry : bond 0.00335 (15414) covalent geometry : angle 0.69653 (20941) SS BOND : bond 0.00288 ( 15) SS BOND : angle 1.24151 ( 30) hydrogen bonds : bond 0.02978 ( 258) hydrogen bonds : angle 6.45866 ( 648) link_ALPHA1-2 : bond 0.02909 ( 2) link_ALPHA1-2 : angle 3.06805 ( 6) link_ALPHA1-3 : bond 0.01098 ( 3) link_ALPHA1-3 : angle 2.37355 ( 9) link_ALPHA1-6 : bond 0.01008 ( 5) link_ALPHA1-6 : angle 2.32002 ( 15) link_BETA1-4 : bond 0.00832 ( 8) link_BETA1-4 : angle 2.31241 ( 24) link_NAG-ASN : bond 0.01011 ( 3) link_NAG-ASN : angle 3.72210 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.7282 (mmm) cc_final: 0.6782 (mmt) REVERT: K 79 GLN cc_start: 0.9016 (pm20) cc_final: 0.8642 (pm20) REVERT: F 81 MET cc_start: 0.6556 (mmm) cc_final: 0.5764 (mmm) REVERT: M 4 MET cc_start: 0.7383 (mmm) cc_final: 0.6049 (mmm) REVERT: I 4 MET cc_start: 0.4400 (tmm) cc_final: 0.3699 (tpt) REVERT: I 49 TYR cc_start: 0.7910 (p90) cc_final: 0.7458 (p90) REVERT: I 85 LEU cc_start: 0.9032 (tp) cc_final: 0.8784 (pp) REVERT: D 173 GLN cc_start: 0.8082 (pm20) cc_final: 0.7819 (pm20) REVERT: A 81 ASP cc_start: 0.6773 (t0) cc_final: 0.6461 (t0) REVERT: A 100 PHE cc_start: 0.7926 (m-80) cc_final: 0.7653 (m-80) REVERT: A 263 MET cc_start: 0.8181 (tmm) cc_final: 0.7909 (tmm) REVERT: B 140 MET cc_start: 0.6507 (ttt) cc_final: 0.6288 (ttm) REVERT: B 404 MET cc_start: 0.9565 (ppp) cc_final: 0.9311 (ppp) REVERT: B 411 MET cc_start: 0.9101 (mmp) cc_final: 0.8708 (mmm) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1235 time to fit residues: 29.7035 Evaluate side-chains 133 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 187 optimal weight: 20.0000 chunk 126 optimal weight: 0.6980 chunk 142 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 80 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN L 43 HIS ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.050888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.042567 restraints weight = 207883.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.042881 restraints weight = 170909.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.042856 restraints weight = 138671.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.043080 restraints weight = 136727.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.043014 restraints weight = 136107.952| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15450 Z= 0.143 Angle : 0.691 9.559 21034 Z= 0.327 Chirality : 0.045 0.307 2411 Planarity : 0.004 0.052 2586 Dihedral : 9.517 107.270 2486 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.18), residues: 1865 helix: -1.57 (0.32), residues: 233 sheet: -2.27 (0.22), residues: 487 loop : -2.13 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 61 TYR 0.024 0.002 TYR J 49 PHE 0.020 0.001 PHE K 62 TRP 0.022 0.002 TRP G 33 HIS 0.015 0.002 HIS J 91 Details of bonding type rmsd covalent geometry : bond 0.00307 (15414) covalent geometry : angle 0.67624 (20941) SS BOND : bond 0.00240 ( 15) SS BOND : angle 0.99917 ( 30) hydrogen bonds : bond 0.02837 ( 258) hydrogen bonds : angle 6.28256 ( 648) link_ALPHA1-2 : bond 0.02271 ( 2) link_ALPHA1-2 : angle 2.96996 ( 6) link_ALPHA1-3 : bond 0.01378 ( 3) link_ALPHA1-3 : angle 2.32885 ( 9) link_ALPHA1-6 : bond 0.00871 ( 5) link_ALPHA1-6 : angle 2.17138 ( 15) link_BETA1-4 : bond 0.00759 ( 8) link_BETA1-4 : angle 2.35292 ( 24) link_NAG-ASN : bond 0.00997 ( 3) link_NAG-ASN : angle 3.72270 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 ASP cc_start: 0.8178 (m-30) cc_final: 0.7956 (m-30) REVERT: K 4 MET cc_start: 0.6918 (mmm) cc_final: 0.6480 (mmt) REVERT: K 79 GLN cc_start: 0.8901 (pm20) cc_final: 0.8437 (pm20) REVERT: F 81 MET cc_start: 0.6690 (mmm) cc_final: 0.5951 (mmm) REVERT: M 4 MET cc_start: 0.7681 (mmm) cc_final: 0.6481 (mmm) REVERT: I 4 MET cc_start: 0.4549 (tmm) cc_final: 0.3551 (tpt) REVERT: I 53 THR cc_start: 0.8071 (m) cc_final: 0.7674 (m) REVERT: I 85 LEU cc_start: 0.9248 (tp) cc_final: 0.8969 (pp) REVERT: I 86 TYR cc_start: 0.7920 (p90) cc_final: 0.7683 (p90) REVERT: A 81 ASP cc_start: 0.7223 (t0) cc_final: 0.6911 (t0) REVERT: A 263 MET cc_start: 0.8197 (tmm) cc_final: 0.7919 (tmm) REVERT: B 140 MET cc_start: 0.6512 (ttt) cc_final: 0.5977 (ttm) REVERT: B 404 MET cc_start: 0.9607 (ppp) cc_final: 0.9354 (ppp) REVERT: B 411 MET cc_start: 0.9217 (mmp) cc_final: 0.8807 (mmp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1168 time to fit residues: 26.7186 Evaluate side-chains 131 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 159 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.050542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.042082 restraints weight = 209954.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.042512 restraints weight = 167419.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.042696 restraints weight = 133886.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.042824 restraints weight = 118562.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.043035 restraints weight = 113451.610| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.7097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15450 Z= 0.138 Angle : 0.693 9.549 21034 Z= 0.330 Chirality : 0.045 0.302 2411 Planarity : 0.004 0.063 2586 Dihedral : 8.930 101.300 2486 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.18), residues: 1865 helix: -1.38 (0.33), residues: 233 sheet: -2.18 (0.22), residues: 473 loop : -2.10 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 31 TYR 0.018 0.002 TYR A 228 PHE 0.026 0.002 PHE C 99 TRP 0.026 0.002 TRP L 33 HIS 0.015 0.002 HIS J 91 Details of bonding type rmsd covalent geometry : bond 0.00304 (15414) covalent geometry : angle 0.67725 (20941) SS BOND : bond 0.00231 ( 15) SS BOND : angle 1.73857 ( 30) hydrogen bonds : bond 0.02785 ( 258) hydrogen bonds : angle 6.18719 ( 648) link_ALPHA1-2 : bond 0.02031 ( 2) link_ALPHA1-2 : angle 3.01906 ( 6) link_ALPHA1-3 : bond 0.01063 ( 3) link_ALPHA1-3 : angle 1.98372 ( 9) link_ALPHA1-6 : bond 0.00922 ( 5) link_ALPHA1-6 : angle 2.13109 ( 15) link_BETA1-4 : bond 0.00816 ( 8) link_BETA1-4 : angle 2.44116 ( 24) link_NAG-ASN : bond 0.00966 ( 3) link_NAG-ASN : angle 3.63729 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.7191 (mmm) cc_final: 0.5885 (mmm) REVERT: K 79 GLN cc_start: 0.8968 (pm20) cc_final: 0.8516 (pm20) REVERT: F 81 MET cc_start: 0.7068 (mmm) cc_final: 0.6306 (mmm) REVERT: M 4 MET cc_start: 0.7919 (mmm) cc_final: 0.6622 (mmm) REVERT: I 4 MET cc_start: 0.4660 (tmm) cc_final: 0.3441 (tpt) REVERT: I 53 THR cc_start: 0.8080 (m) cc_final: 0.7707 (m) REVERT: I 85 LEU cc_start: 0.9286 (tp) cc_final: 0.8940 (pp) REVERT: I 86 TYR cc_start: 0.7851 (p90) cc_final: 0.7589 (p90) REVERT: A 81 ASP cc_start: 0.7148 (t0) cc_final: 0.6835 (t0) REVERT: A 263 MET cc_start: 0.8281 (tmm) cc_final: 0.8038 (tmm) REVERT: B 140 MET cc_start: 0.6742 (ttt) cc_final: 0.6516 (ttm) REVERT: B 411 MET cc_start: 0.9142 (mmp) cc_final: 0.8734 (mmp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1183 time to fit residues: 25.9221 Evaluate side-chains 131 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 186 optimal weight: 30.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 HIS ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.047850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.040628 restraints weight = 237758.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.041030 restraints weight = 177817.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.041333 restraints weight = 146445.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.041553 restraints weight = 127747.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.041636 restraints weight = 116797.915| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.8677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 15450 Z= 0.253 Angle : 0.858 11.824 21034 Z= 0.421 Chirality : 0.050 0.317 2411 Planarity : 0.006 0.058 2586 Dihedral : 8.835 93.525 2486 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.18), residues: 1865 helix: -1.18 (0.34), residues: 231 sheet: -2.61 (0.21), residues: 520 loop : -2.08 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 61 TYR 0.023 0.003 TYR M 36 PHE 0.040 0.003 PHE C 99 TRP 0.033 0.003 TRP F 33 HIS 0.021 0.003 HIS J 91 Details of bonding type rmsd covalent geometry : bond 0.00556 (15414) covalent geometry : angle 0.84399 (20941) SS BOND : bond 0.01099 ( 15) SS BOND : angle 2.06088 ( 30) hydrogen bonds : bond 0.03834 ( 258) hydrogen bonds : angle 6.78563 ( 648) link_ALPHA1-2 : bond 0.01871 ( 2) link_ALPHA1-2 : angle 3.06726 ( 6) link_ALPHA1-3 : bond 0.00949 ( 3) link_ALPHA1-3 : angle 2.16044 ( 9) link_ALPHA1-6 : bond 0.00956 ( 5) link_ALPHA1-6 : angle 2.22622 ( 15) link_BETA1-4 : bond 0.00835 ( 8) link_BETA1-4 : angle 2.67505 ( 24) link_NAG-ASN : bond 0.00560 ( 3) link_NAG-ASN : angle 3.51119 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.5432 (mmm) cc_final: 0.3568 (ptp) REVERT: K 55 HIS cc_start: 0.9231 (t70) cc_final: 0.8986 (t70) REVERT: K 79 GLN cc_start: 0.8302 (pm20) cc_final: 0.7707 (pm20) REVERT: M 4 MET cc_start: 0.8412 (mmm) cc_final: 0.7401 (mmm) REVERT: I 4 MET cc_start: 0.4852 (tmm) cc_final: 0.3550 (tpt) REVERT: A 81 ASP cc_start: 0.8147 (t0) cc_final: 0.7566 (m-30) REVERT: A 263 MET cc_start: 0.8468 (tmm) cc_final: 0.8198 (tmm) REVERT: B 8 MET cc_start: 0.7434 (tpt) cc_final: 0.7186 (tpt) REVERT: B 56 MET cc_start: 0.8296 (mmp) cc_final: 0.8019 (mmp) REVERT: B 140 MET cc_start: 0.7346 (ttt) cc_final: 0.6915 (ttm) REVERT: B 411 MET cc_start: 0.8766 (mmp) cc_final: 0.8503 (mmp) REVERT: C 163 MET cc_start: 0.6833 (mmp) cc_final: 0.6462 (mmt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1258 time to fit residues: 24.9440 Evaluate side-chains 114 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 8 optimal weight: 3.9990 chunk 123 optimal weight: 30.0000 chunk 74 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 101 optimal weight: 0.0020 chunk 5 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 131 optimal weight: 20.0000 chunk 133 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 overall best weight: 2.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.049227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.040670 restraints weight = 211582.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.041030 restraints weight = 172330.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.041159 restraints weight = 139348.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.041168 restraints weight = 125328.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.041335 restraints weight = 124754.519| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.8698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15450 Z= 0.146 Angle : 0.748 10.706 21034 Z= 0.355 Chirality : 0.047 0.313 2411 Planarity : 0.004 0.054 2586 Dihedral : 8.510 90.248 2486 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.18), residues: 1865 helix: -1.28 (0.33), residues: 238 sheet: -2.51 (0.21), residues: 524 loop : -2.00 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 54 TYR 0.033 0.002 TYR F 32 PHE 0.025 0.002 PHE K 62 TRP 0.022 0.002 TRP L 33 HIS 0.017 0.002 HIS J 91 Details of bonding type rmsd covalent geometry : bond 0.00325 (15414) covalent geometry : angle 0.73329 (20941) SS BOND : bond 0.00297 ( 15) SS BOND : angle 1.70073 ( 30) hydrogen bonds : bond 0.03050 ( 258) hydrogen bonds : angle 6.60809 ( 648) link_ALPHA1-2 : bond 0.02116 ( 2) link_ALPHA1-2 : angle 3.13926 ( 6) link_ALPHA1-3 : bond 0.00968 ( 3) link_ALPHA1-3 : angle 1.88669 ( 9) link_ALPHA1-6 : bond 0.01017 ( 5) link_ALPHA1-6 : angle 2.14774 ( 15) link_BETA1-4 : bond 0.00774 ( 8) link_BETA1-4 : angle 2.49924 ( 24) link_NAG-ASN : bond 0.00980 ( 3) link_NAG-ASN : angle 3.48209 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.7489 (mmm) cc_final: 0.5809 (ptp) REVERT: K 79 GLN cc_start: 0.8794 (pm20) cc_final: 0.8272 (pm20) REVERT: M 4 MET cc_start: 0.8220 (mmm) cc_final: 0.6830 (mmm) REVERT: I 4 MET cc_start: 0.4418 (tmm) cc_final: 0.3143 (tpt) REVERT: D 173 GLN cc_start: 0.8270 (pm20) cc_final: 0.8032 (pm20) REVERT: A 81 ASP cc_start: 0.7529 (t0) cc_final: 0.7282 (t70) REVERT: A 263 MET cc_start: 0.8553 (tmm) cc_final: 0.8258 (tmm) REVERT: B 140 MET cc_start: 0.6981 (ttt) cc_final: 0.6644 (ttm) REVERT: B 404 MET cc_start: 0.9573 (ppp) cc_final: 0.9341 (ppp) REVERT: B 411 MET cc_start: 0.9071 (mmp) cc_final: 0.8664 (mmp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1206 time to fit residues: 24.3152 Evaluate side-chains 118 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.047743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.039341 restraints weight = 214232.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.039645 restraints weight = 174903.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.039645 restraints weight = 145217.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.039646 restraints weight = 145191.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.039646 restraints weight = 145084.805| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.9479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15450 Z= 0.244 Angle : 0.835 11.783 21034 Z= 0.406 Chirality : 0.049 0.305 2411 Planarity : 0.005 0.049 2586 Dihedral : 8.398 82.750 2486 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.18), residues: 1865 helix: -1.13 (0.34), residues: 236 sheet: -2.71 (0.21), residues: 512 loop : -2.13 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 61 TYR 0.027 0.003 TYR A 222 PHE 0.028 0.002 PHE A 100 TRP 0.032 0.003 TRP G 33 HIS 0.022 0.003 HIS J 91 Details of bonding type rmsd covalent geometry : bond 0.00535 (15414) covalent geometry : angle 0.82193 (20941) SS BOND : bond 0.00493 ( 15) SS BOND : angle 1.72292 ( 30) hydrogen bonds : bond 0.03858 ( 258) hydrogen bonds : angle 6.93113 ( 648) link_ALPHA1-2 : bond 0.01880 ( 2) link_ALPHA1-2 : angle 3.13210 ( 6) link_ALPHA1-3 : bond 0.00846 ( 3) link_ALPHA1-3 : angle 1.98463 ( 9) link_ALPHA1-6 : bond 0.00969 ( 5) link_ALPHA1-6 : angle 2.17773 ( 15) link_BETA1-4 : bond 0.00813 ( 8) link_BETA1-4 : angle 2.67526 ( 24) link_NAG-ASN : bond 0.00629 ( 3) link_NAG-ASN : angle 3.42922 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2516.10 seconds wall clock time: 44 minutes 31.27 seconds (2671.27 seconds total)