Starting phenix.real_space_refine on Fri Jul 3 16:59:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mlv_23911/07_2026/7mlv_23911.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mlv_23911/07_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_23911/07_2026/7mlv_23911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mlv_23911/07_2026/7mlv_23911.map" model { file = "/net/cci-nas-00/data/ceres_data/7mlv_23911/07_2026/7mlv_23911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mlv_23911/07_2026/7mlv_23911.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mlv_23911/07_2026/7mlv_23911.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mlv_23911/07_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-6108/lib/python3.11/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 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 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 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 chiralities: 7 Time building chain proxies: 3.25, per 1000 atoms: 0.22 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: 1.03 Conformation dependent library (CDL) restraints added in 677.2 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: 0.37 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: 1.77 Time building geometry restraints manager: 1.41 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 - 15.33: 8287 15.33 - 30.66: 451 30.66 - 45.99: 117 45.99 - 61.32: 13 61.32 - 76.65: 15 Dihedral angle restraints: 8883 sinusoidal: 3335 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 8880 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.670 Find NCS groups from input model: 0.190 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4056 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 : 10.905 76.646 5280 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/Z covalent geometry : bond 0.00482 / 0.26 (15414) covalent geometry : angle 1.02499 / 0.53 (20941) SS BOND : bond 0.00446 / 0.23 ( 15) SS BOND : angle 2.03764 / 1.45 ( 30) hydrogen bonds : bond 0.32868 / 22.88 ( 258) hydrogen bonds : angle 12.55208 / 8.87 ( 648) link_ALPHA1-2 : bond 0.01043 / 0.52 ( 2) link_ALPHA1-2 : angle 1.68161 / 0.95 ( 6) link_ALPHA1-3 : bond 0.00828 / 0.35 ( 3) link_ALPHA1-3 : angle 1.89084 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00715 / 0.37 ( 5) link_ALPHA1-6 : angle 2.43784 / 1.15 ( 15) link_BETA1-4 : bond 0.01014 / 0.44 ( 8) link_BETA1-4 : angle 3.85944 / 2.36 ( 24) link_NAG-ASN : bond 0.14805 / 5.95 ( 3) link_NAG-ASN : angle 17.02646 / 9.47 ( 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 : 0.607 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: 0.1397 time to fit residues: 48.2966 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 : 0.557 ------------------------------------------------------------------------------- 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... ** 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 = 0.3950 r_free = 0.3950 target = 0.055224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.048640 restraints weight = 214748.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.049170 restraints weight = 179847.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.049470 restraints weight = 142123.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.049648 restraints weight = 127193.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.049778 restraints weight = 113561.901| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5387 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15450 Z= 0.160 Angle : 0.709 12.475 21034 Z= 0.350 Chirality : 0.045 0.289 2411 Planarity : 0.005 0.077 2586 Dihedral : 5.614 23.789 2052 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.19 % Allowed : 4.44 % Favored : 95.37 % 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: -3.66 (0.21), residues: 237 sheet: -2.37 (0.21), residues: 484 loop : -3.06 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG M 18 TYR 0.020 0.002 TYR J 49 PHE 0.017 0.002 PHE G 70 TRP 0.022 0.002 TRP F 108 HIS 0.004 0.001 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (15414) covalent geometry : angle 0.69323 / 0.35 (20941) SS BOND : bond 0.00325 / 0.18 ( 15) SS BOND : angle 1.01657 / 0.72 ( 30) hydrogen bonds : bond 0.04069 / 2.87 ( 258) hydrogen bonds : angle 8.24958 / 5.82 ( 648) link_ALPHA1-2 : bond 0.00680 / 0.33 ( 2) link_ALPHA1-2 : angle 1.37340 / 0.71 ( 6) link_ALPHA1-3 : bond 0.00729 / 0.34 ( 3) link_ALPHA1-3 : angle 2.68763 / 1.30 ( 9) link_ALPHA1-6 : bond 0.00492 / 0.25 ( 5) link_ALPHA1-6 : angle 2.03592 / 1.00 ( 15) link_BETA1-4 : bond 0.01118 / 0.39 ( 8) link_BETA1-4 : angle 2.52275 / 1.58 ( 24) link_NAG-ASN : bond 0.01393 / 0.61 ( 3) link_NAG-ASN : angle 4.48942 / 1.93 ( 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: 3 poor density : 184 time to evaluate : 0.583 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: 0.7431 (tp) cc_final: 0.7011 (tp) REVERT: K 3 VAL cc_start: 0.7992 (m) cc_final: 0.7481 (m) REVERT: K 4 MET cc_start: 0.3101 (mmm) cc_final: 0.2711 (tpt) REVERT: M 4 MET cc_start: 0.6364 (mmm) cc_final: 0.5972 (mmm) REVERT: I 4 MET cc_start: 0.3717 (tmm) cc_final: 0.2971 (tpt) REVERT: D 173 GLN cc_start: 0.7830 (pm20) cc_final: 0.7316 (pm20) REVERT: A 18 MET cc_start: 0.6187 (tmm) cc_final: 0.5983 (tmm) REVERT: B 202 TYR cc_start: 0.5896 (m-80) cc_final: 0.5634 (m-80) REVERT: B 411 MET cc_start: 0.8799 (mmp) cc_final: 0.8397 (mmm) REVERT: C 200 LYS cc_start: 0.6006 (mtmm) cc_final: 0.4770 (mtmm) outliers start: 3 outliers final: 1 residues processed: 187 average time/residue: 0.1464 time to fit residues: 38.7216 Evaluate side-chains 145 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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: 0.8980 chunk 127 optimal weight: 40.0000 chunk 185 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.052759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.044221 restraints weight = 205024.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.044620 restraints weight = 165487.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.044765 restraints weight = 133177.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.044931 restraints weight = 121074.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.045153 restraints weight = 111907.594| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15450 Z= 0.206 Angle : 0.775 13.892 21034 Z= 0.387 Chirality : 0.048 0.328 2411 Planarity : 0.006 0.078 2586 Dihedral : 5.808 35.788 2052 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.92 (0.17), residues: 1865 helix: -2.87 (0.27), residues: 239 sheet: -2.46 (0.20), residues: 549 loop : -2.66 (0.16), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 61 TYR 0.023 0.002 TYR D 128 PHE 0.032 0.003 PHE B 242 TRP 0.080 0.003 TRP B 239 HIS 0.012 0.002 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (15414) covalent geometry : angle 0.76389 / 0.38 (20941) SS BOND : bond 0.00750 / 0.39 ( 15) SS BOND : angle 1.64314 / 1.04 ( 30) hydrogen bonds : bond 0.04382 / 3.12 ( 258) hydrogen bonds : angle 7.27128 / 5.07 ( 648) link_ALPHA1-2 : bond 0.01028 / 0.49 ( 2) link_ALPHA1-2 : angle 1.03934 / 0.59 ( 6) link_ALPHA1-3 : bond 0.01069 / 0.45 ( 3) link_ALPHA1-3 : angle 1.71639 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00591 / 0.31 ( 5) link_ALPHA1-6 : angle 1.76839 / 0.96 ( 15) link_BETA1-4 : bond 0.01203 / 0.45 ( 8) link_BETA1-4 : angle 2.32392 / 1.43 ( 24) link_NAG-ASN : bond 0.01159 / 0.49 ( 3) link_NAG-ASN : angle 3.56535 / 1.62 ( 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 174 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.627 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: G 81 MET cc_start: 0.8004 (tpt) cc_final: 0.7794 (tpp) REVERT: G 101 ARG cc_start: 0.5674 (tpt170) cc_final: 0.5455 (tpt170) REVERT: M 4 MET cc_start: 0.6971 (mmm) cc_final: 0.5897 (mmm) REVERT: L 81 MET cc_start: 0.4202 (tpt) cc_final: 0.3961 (tpt) REVERT: L 98 MET cc_start: 0.5049 (ttt) cc_final: 0.4482 (ttt) REVERT: I 4 MET cc_start: 0.4327 (tmm) cc_final: 0.3246 (tpt) REVERT: I 53 THR cc_start: 0.8221 (m) cc_final: 0.7999 (m) REVERT: D 173 GLN cc_start: 0.7958 (pm20) cc_final: 0.7749 (pm20) REVERT: A 18 MET cc_start: 0.5949 (tmm) cc_final: 0.5745 (tmm) REVERT: A 81 ASP cc_start: 0.6559 (t0) cc_final: 0.6271 (t70) REVERT: B 140 MET cc_start: 0.5871 (ttt) cc_final: 0.5513 (ttm) REVERT: B 404 MET cc_start: 0.9565 (ppp) cc_final: 0.9336 (ppp) REVERT: B 411 MET cc_start: 0.9089 (mmp) cc_final: 0.8744 (mmm) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.1358 time to fit residues: 34.4898 Evaluate side-chains 135 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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: 0.3980 chunk 139 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 86 optimal weight: 0.4980 chunk 119 optimal weight: 0.1980 chunk 50 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** I 90 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** ** A 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 = 0.3875 r_free = 0.3875 target = 0.053013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.044497 restraints weight = 204865.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.044880 restraints weight = 168278.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.045047 restraints weight = 137709.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.045238 restraints weight = 121815.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.045238 restraints weight = 111840.224| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.4884 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= 0.113 Angle : 0.667 11.527 21034 Z= 0.320 Chirality : 0.044 0.293 2411 Planarity : 0.004 0.050 2586 Dihedral : 5.395 31.078 2052 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.64 (0.17), residues: 1865 helix: -2.35 (0.29), residues: 237 sheet: -2.41 (0.20), residues: 545 loop : -2.48 (0.16), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 101 TYR 0.025 0.001 TYR F 80 PHE 0.015 0.001 PHE K 62 TRP 0.023 0.002 TRP B 239 HIS 0.008 0.001 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (15414) covalent geometry : angle 0.65528 / 0.32 (20941) SS BOND : bond 0.00203 / 0.11 ( 15) SS BOND : angle 1.01456 / 0.68 ( 30) hydrogen bonds : bond 0.03132 / 2.25 ( 258) hydrogen bonds : angle 6.79724 / 4.73 ( 648) link_ALPHA1-2 : bond 0.00730 / 0.36 ( 2) link_ALPHA1-2 : angle 1.18137 / 0.65 ( 6) link_ALPHA1-3 : bond 0.00735 / 0.33 ( 3) link_ALPHA1-3 : angle 1.86342 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00532 / 0.28 ( 5) link_ALPHA1-6 : angle 1.64494 / 0.88 ( 15) link_BETA1-4 : bond 0.00834 / 0.32 ( 8) link_BETA1-4 : angle 2.21066 / 1.38 ( 24) link_NAG-ASN : bond 0.01004 / 0.46 ( 3) link_NAG-ASN : angle 4.08457 / 1.75 ( 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 : 0.586 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: K 4 MET cc_start: 0.7394 (mmm) cc_final: 0.5874 (mmm) REVERT: M 4 MET cc_start: 0.6966 (mmm) cc_final: 0.5993 (mmm) REVERT: L 98 MET cc_start: 0.5159 (ttt) cc_final: 0.4747 (ttt) REVERT: I 4 MET cc_start: 0.4233 (tmm) cc_final: 0.3386 (tpt) REVERT: I 87 TYR cc_start: 0.7695 (m-80) cc_final: 0.7466 (m-80) REVERT: D 173 GLN cc_start: 0.8045 (pm20) cc_final: 0.7737 (pm20) REVERT: A 81 ASP cc_start: 0.5996 (t0) cc_final: 0.5709 (t0) REVERT: B 404 MET cc_start: 0.9558 (ppp) cc_final: 0.9307 (ppp) REVERT: B 411 MET cc_start: 0.9060 (mmp) cc_final: 0.8586 (mmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1150 time to fit residues: 27.7425 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 : 0.349 ------------------------------------------------------------------------------- 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: 20.0000 chunk 124 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** G 5 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 HIS ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.048604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.041363 restraints weight = 237779.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.041763 restraints weight = 177733.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.042078 restraints weight = 147921.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.042311 restraints weight = 128131.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.042432 restraints weight = 116794.464| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 15450 Z= 0.296 Angle : 0.868 14.025 21034 Z= 0.438 Chirality : 0.051 0.306 2411 Planarity : 0.006 0.080 2586 Dihedral : 6.227 29.637 2052 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 0.13 % Allowed : 3.79 % Favored : 96.08 % 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: -1.93 (0.31), residues: 243 sheet: -2.76 (0.20), residues: 522 loop : -2.41 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 213 TYR 0.025 0.003 TYR F 80 PHE 0.036 0.003 PHE G 64 TRP 0.036 0.003 TRP F 33 HIS 0.029 0.003 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.30 (15414) covalent geometry : angle 0.85815 / 0.44 (20941) SS BOND : bond 0.00751 / 0.40 ( 15) SS BOND : angle 1.72043 / 1.15 ( 30) hydrogen bonds : bond 0.04208 / 2.87 ( 258) hydrogen bonds : angle 7.16210 / 4.93 ( 648) link_ALPHA1-2 : bond 0.00677 / 0.34 ( 2) link_ALPHA1-2 : angle 1.26033 / 0.68 ( 6) link_ALPHA1-3 : bond 0.00399 / 0.19 ( 3) link_ALPHA1-3 : angle 1.72943 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00444 / 0.21 ( 5) link_ALPHA1-6 : angle 1.80749 / 0.95 ( 15) link_BETA1-4 : bond 0.01108 / 0.46 ( 8) link_BETA1-4 : angle 2.40407 / 1.42 ( 24) link_NAG-ASN : bond 0.00837 / 0.40 ( 3) link_NAG-ASN : angle 3.78622 / 1.61 ( 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 149 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.965 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: J 53 THR cc_start: 0.8713 (m) cc_final: 0.8496 (p) REVERT: K 79 GLN cc_start: 0.8380 (pm20) cc_final: 0.7883 (pm20) REVERT: F 80 TYR cc_start: 0.8933 (m-80) cc_final: 0.8559 (m-80) REVERT: M 4 MET cc_start: 0.8035 (mmm) cc_final: 0.6811 (mmm) REVERT: I 4 MET cc_start: 0.4778 (tmm) cc_final: 0.3561 (tpt) REVERT: A 81 ASP cc_start: 0.7608 (t0) cc_final: 0.7312 (t0) REVERT: A 163 MET cc_start: 0.8220 (mmm) cc_final: 0.7787 (mmm) REVERT: B 140 MET cc_start: 0.6819 (ttt) cc_final: 0.6501 (ttm) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.1351 time to fit residues: 29.2114 Evaluate side-chains 117 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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: 0.0030 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 164 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 128 optimal weight: 40.0000 chunk 174 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** I 55 HIS ** 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.050060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.041532 restraints weight = 209924.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.041843 restraints weight = 168172.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.042135 restraints weight = 135016.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.042135 restraints weight = 116564.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.042135 restraints weight = 116564.650| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15450 Z= 0.124 Angle : 0.698 10.639 21034 Z= 0.337 Chirality : 0.045 0.304 2411 Planarity : 0.004 0.066 2586 Dihedral : 5.666 27.496 2052 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: -3.39 (0.17), residues: 1865 helix: -1.80 (0.31), residues: 238 sheet: -2.44 (0.22), residues: 486 loop : -2.32 (0.16), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 31 TYR 0.023 0.002 TYR F 80 PHE 0.026 0.002 PHE C 99 TRP 0.021 0.001 TRP G 33 HIS 0.015 0.001 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (15414) covalent geometry : angle 0.68791 / 0.33 (20941) SS BOND : bond 0.00292 / 0.18 ( 15) SS BOND : angle 1.23217 / 0.86 ( 30) hydrogen bonds : bond 0.03040 / 2.14 ( 258) hydrogen bonds : angle 6.60409 / 4.56 ( 648) link_ALPHA1-2 : bond 0.00787 / 0.39 ( 2) link_ALPHA1-2 : angle 1.16901 / 0.65 ( 6) link_ALPHA1-3 : bond 0.00708 / 0.33 ( 3) link_ALPHA1-3 : angle 1.69744 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00554 / 0.28 ( 5) link_ALPHA1-6 : angle 1.61260 / 0.87 ( 15) link_BETA1-4 : bond 0.00813 / 0.29 ( 8) link_BETA1-4 : angle 2.15437 / 1.31 ( 24) link_NAG-ASN : bond 0.01121 / 0.49 ( 3) link_NAG-ASN : angle 3.61410 / 1.56 ( 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 146 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.619 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: K 4 MET cc_start: 0.7292 (mmm) cc_final: 0.5943 (mmm) REVERT: K 79 GLN cc_start: 0.8987 (pm20) cc_final: 0.8516 (pm20) REVERT: F 81 MET cc_start: 0.6651 (mmm) cc_final: 0.5975 (mmm) REVERT: M 4 MET cc_start: 0.8099 (mmm) cc_final: 0.6773 (mmm) REVERT: I 4 MET cc_start: 0.4597 (tmm) cc_final: 0.3236 (tpt) REVERT: A 81 ASP cc_start: 0.7029 (t0) cc_final: 0.6711 (t0) REVERT: B 140 MET cc_start: 0.6525 (ttt) cc_final: 0.6188 (ttm) REVERT: B 404 MET cc_start: 0.9542 (ppp) cc_final: 0.9277 (ppp) REVERT: B 411 MET cc_start: 0.9051 (mmp) cc_final: 0.8750 (mmm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1186 time to fit residues: 26.4781 Evaluate side-chains 123 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 2.9990 chunk 142 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 HIS ** 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 102 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.049372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.040916 restraints weight = 214111.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.041169 restraints weight = 169471.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.041481 restraints weight = 138778.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.041560 restraints weight = 119919.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.041700 restraints weight = 112557.315| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.7554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15450 Z= 0.153 Angle : 0.688 10.298 21034 Z= 0.336 Chirality : 0.044 0.297 2411 Planarity : 0.004 0.051 2586 Dihedral : 5.606 28.257 2052 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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 (0.18), residues: 1865 helix: -1.57 (0.32), residues: 239 sheet: -2.48 (0.21), residues: 522 loop : -2.22 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 101 TYR 0.026 0.002 TYR I 49 PHE 0.023 0.002 PHE C 99 TRP 0.025 0.002 TRP L 33 HIS 0.016 0.002 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15414) covalent geometry : angle 0.67774 / 0.33 (20941) SS BOND : bond 0.00263 / 0.16 ( 15) SS BOND : angle 1.17346 / 0.70 ( 30) hydrogen bonds : bond 0.03014 / 2.10 ( 258) hydrogen bonds : angle 6.55469 / 4.54 ( 648) link_ALPHA1-2 : bond 0.00756 / 0.37 ( 2) link_ALPHA1-2 : angle 1.14061 / 0.61 ( 6) link_ALPHA1-3 : bond 0.00719 / 0.31 ( 3) link_ALPHA1-3 : angle 1.74069 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00505 / 0.25 ( 5) link_ALPHA1-6 : angle 1.64497 / 0.89 ( 15) link_BETA1-4 : bond 0.00795 / 0.33 ( 8) link_BETA1-4 : angle 2.14745 / 1.30 ( 24) link_NAG-ASN : bond 0.00924 / 0.41 ( 3) link_NAG-ASN : angle 3.65664 / 1.56 ( 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 137 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.673 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: J 53 THR cc_start: 0.8261 (p) cc_final: 0.7910 (p) REVERT: G 28 THR cc_start: 0.6045 (p) cc_final: 0.5622 (p) REVERT: K 79 GLN cc_start: 0.8950 (pm20) cc_final: 0.8499 (pm20) REVERT: M 4 MET cc_start: 0.8138 (mmm) cc_final: 0.6848 (mmm) REVERT: I 4 MET cc_start: 0.4594 (tmm) cc_final: 0.3275 (tpt) REVERT: H 13 LYS cc_start: 0.8681 (mmpt) cc_final: 0.8458 (mmtt) REVERT: A 81 ASP cc_start: 0.7374 (t0) cc_final: 0.7071 (t0) REVERT: B 140 MET cc_start: 0.6673 (ttt) cc_final: 0.6057 (ttm) REVERT: B 404 MET cc_start: 0.9568 (ppp) cc_final: 0.9310 (ppp) REVERT: B 411 MET cc_start: 0.9081 (mmp) cc_final: 0.8781 (mmm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1091 time to fit residues: 23.3290 Evaluate side-chains 119 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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: 3.9990 chunk 21 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.049502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.040980 restraints weight = 214067.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.041351 restraints weight = 169683.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.041531 restraints weight = 136079.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.041531 restraints weight = 119605.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.041531 restraints weight = 119597.751| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.7898 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= 0.130 Angle : 0.687 9.764 21034 Z= 0.332 Chirality : 0.044 0.295 2411 Planarity : 0.004 0.048 2586 Dihedral : 5.502 27.744 2052 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -1.35 (0.33), residues: 231 sheet: -2.44 (0.21), residues: 537 loop : -2.03 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 31 TYR 0.035 0.002 TYR F 32 PHE 0.021 0.001 PHE K 62 TRP 0.019 0.001 TRP L 33 HIS 0.008 0.001 HIS F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15414) covalent geometry : angle 0.67429 / 0.33 (20941) SS BOND : bond 0.00274 / 0.13 ( 15) SS BOND : angle 1.96228 / 1.45 ( 30) hydrogen bonds : bond 0.02987 / 2.10 ( 258) hydrogen bonds : angle 6.37916 / 4.43 ( 648) link_ALPHA1-2 : bond 0.00721 / 0.36 ( 2) link_ALPHA1-2 : angle 1.21589 / 0.65 ( 6) link_ALPHA1-3 : bond 0.00657 / 0.30 ( 3) link_ALPHA1-3 : angle 1.66154 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00519 / 0.26 ( 5) link_ALPHA1-6 : angle 1.60291 / 0.88 ( 15) link_BETA1-4 : bond 0.00768 / 0.28 ( 8) link_BETA1-4 : angle 2.10020 / 1.28 ( 24) link_NAG-ASN : bond 0.01000 / 0.44 ( 3) link_NAG-ASN : angle 3.58043 / 1.53 ( 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 139 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.610 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 79 GLN cc_start: 0.8921 (pm20) cc_final: 0.8412 (pm20) REVERT: F 81 MET cc_start: 0.6623 (mmm) cc_final: 0.5876 (mmm) REVERT: M 4 MET cc_start: 0.8157 (mmm) cc_final: 0.6796 (mmm) REVERT: I 4 MET cc_start: 0.4322 (tmm) cc_final: 0.2994 (tpt) REVERT: A 81 ASP cc_start: 0.7389 (t0) cc_final: 0.7082 (t0) REVERT: B 140 MET cc_start: 0.6571 (ttt) cc_final: 0.6019 (ttm) REVERT: B 404 MET cc_start: 0.9580 (ppp) cc_final: 0.9340 (ppp) REVERT: B 411 MET cc_start: 0.9076 (mmp) cc_final: 0.8656 (mmp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1113 time to fit residues: 23.7209 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 : 0.596 ------------------------------------------------------------------------------- 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: 7.9990 chunk 111 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN ** 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 8 HIS ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN L 77 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN C 203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.047058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.039891 restraints weight = 237654.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.040275 restraints weight = 178501.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.040450 restraints weight = 147535.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.040711 restraints weight = 134055.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.040806 restraints weight = 121563.159| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.9360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.149 15450 Z= 0.298 Angle : 0.888 12.402 21034 Z= 0.444 Chirality : 0.051 0.493 2411 Planarity : 0.006 0.147 2586 Dihedral : 6.483 39.616 2052 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 0.06 % Allowed : 1.41 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.42 (0.18), residues: 1865 helix: -1.24 (0.33), residues: 236 sheet: -2.89 (0.20), residues: 533 loop : -2.19 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG G 31 TYR 0.030 0.003 TYR G 32 PHE 0.027 0.003 PHE A 100 TRP 0.043 0.003 TRP G 33 HIS 0.019 0.003 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.30 (15414) covalent geometry : angle 0.87818 / 0.44 (20941) SS BOND : bond 0.00629 / 0.34 ( 15) SS BOND : angle 1.94535 / 1.34 ( 30) hydrogen bonds : bond 0.04255 / 2.93 ( 258) hydrogen bonds : angle 7.09259 / 4.92 ( 648) link_ALPHA1-2 : bond 0.00704 / 0.35 ( 2) link_ALPHA1-2 : angle 1.16116 / 0.61 ( 6) link_ALPHA1-3 : bond 0.00657 / 0.29 ( 3) link_ALPHA1-3 : angle 1.88880 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00432 / 0.20 ( 5) link_ALPHA1-6 : angle 1.85369 / 0.96 ( 15) link_BETA1-4 : bond 0.00910 / 0.33 ( 8) link_BETA1-4 : angle 2.39891 / 1.42 ( 24) link_NAG-ASN : bond 0.00579 / 0.28 ( 3) link_NAG-ASN : angle 3.26145 / 1.62 ( 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 123 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 55 HIS cc_start: 0.9296 (t-90) cc_final: 0.8843 (t70) REVERT: K 79 GLN cc_start: 0.8479 (pm20) cc_final: 0.7820 (pm20) REVERT: F 94 TYR cc_start: 0.8731 (m-80) cc_final: 0.8523 (m-80) REVERT: M 4 MET cc_start: 0.8544 (mmm) cc_final: 0.7569 (mmm) REVERT: I 4 MET cc_start: 0.4308 (tmm) cc_final: 0.3027 (tpt) REVERT: I 86 TYR cc_start: 0.7717 (p90) cc_final: 0.7496 (p90) REVERT: H 11 LEU cc_start: 0.6085 (tp) cc_final: 0.5734 (tp) REVERT: B 56 MET cc_start: 0.8373 (mmp) cc_final: 0.8077 (mmp) REVERT: B 140 MET cc_start: 0.7254 (ttt) cc_final: 0.6814 (ttm) REVERT: B 411 MET cc_start: 0.8727 (mmp) cc_final: 0.8471 (mmp) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1084 time to fit residues: 20.4432 Evaluate side-chains 107 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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: 0.8980 chunk 123 optimal weight: 40.0000 chunk 74 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 144 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 147 optimal weight: 0.1980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN ** 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 55 HIS D 115 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.048182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.041081 restraints weight = 230171.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.041516 restraints weight = 171697.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.041830 restraints weight = 141891.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.041949 restraints weight = 124123.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.042131 restraints weight = 115021.427| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.9276 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= 0.140 Angle : 0.752 10.461 21034 Z= 0.362 Chirality : 0.047 0.327 2411 Planarity : 0.004 0.055 2586 Dihedral : 5.967 32.077 2052 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.16 (0.18), residues: 1865 helix: -1.26 (0.33), residues: 235 sheet: -2.54 (0.21), residues: 513 loop : -2.09 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 54 TYR 0.021 0.002 TYR I 49 PHE 0.024 0.002 PHE K 62 TRP 0.026 0.002 TRP C 170 HIS 0.008 0.001 HIS G 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (15414) covalent geometry : angle 0.74116 / 0.36 (20941) SS BOND : bond 0.00279 / 0.14 ( 15) SS BOND : angle 1.58895 / 1.11 ( 30) hydrogen bonds : bond 0.03088 / 2.18 ( 258) hydrogen bonds : angle 6.71936 / 4.70 ( 648) link_ALPHA1-2 : bond 0.00759 / 0.38 ( 2) link_ALPHA1-2 : angle 1.22781 / 0.67 ( 6) link_ALPHA1-3 : bond 0.00644 / 0.29 ( 3) link_ALPHA1-3 : angle 1.64815 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00545 / 0.27 ( 5) link_ALPHA1-6 : angle 1.64006 / 0.88 ( 15) link_BETA1-4 : bond 0.00902 / 0.32 ( 8) link_BETA1-4 : angle 2.12229 / 1.29 ( 24) link_NAG-ASN : bond 0.01063 / 0.47 ( 3) link_NAG-ASN : angle 3.66303 / 1.52 ( 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 126 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 49 TYR cc_start: 0.8231 (p90) cc_final: 0.7894 (p90) REVERT: J 53 THR cc_start: 0.8380 (p) cc_final: 0.8179 (p) REVERT: K 55 HIS cc_start: 0.9218 (t-90) cc_final: 0.8769 (t70) REVERT: K 79 GLN cc_start: 0.8364 (pm20) cc_final: 0.7806 (pm20) REVERT: M 4 MET cc_start: 0.8176 (mmm) cc_final: 0.6850 (mmm) REVERT: I 4 MET cc_start: 0.3738 (tmm) cc_final: 0.2630 (tpt) REVERT: I 86 TYR cc_start: 0.7518 (p90) cc_final: 0.7242 (p90) REVERT: B 140 MET cc_start: 0.6795 (ttt) cc_final: 0.6590 (ttm) REVERT: B 411 MET cc_start: 0.8632 (mmp) cc_final: 0.8420 (mmm) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.1141 time to fit residues: 22.3181 Evaluate side-chains 110 residues out of total 1673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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: 5.9990 chunk 121 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 84 optimal weight: 40.0000 chunk 63 optimal weight: 0.0050 chunk 134 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 overall best weight: 5.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.3714 r_free = 0.3714 target = 0.047103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.040010 restraints weight = 236841.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.040425 restraints weight = 177719.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.040743 restraints weight = 146631.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.040855 restraints weight = 128048.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.040858 restraints weight = 119494.904| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.9930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15450 Z= 0.227 Angle : 0.801 11.327 21034 Z= 0.394 Chirality : 0.047 0.318 2411 Planarity : 0.005 0.102 2586 Dihedral : 6.155 29.582 2052 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -3.33 (0.18), residues: 1865 helix: -1.05 (0.34), residues: 232 sheet: -2.80 (0.20), residues: 526 loop : -2.19 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 101 TYR 0.027 0.003 TYR I 49 PHE 0.022 0.002 PHE K 62 TRP 0.035 0.003 TRP L 33 HIS 0.015 0.002 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (15414) covalent geometry : angle 0.79138 / 0.39 (20941) SS BOND : bond 0.00479 / 0.28 ( 15) SS BOND : angle 1.66267 / 1.16 ( 30) hydrogen bonds : bond 0.03573 / 2.48 ( 258) hydrogen bonds : angle 6.87292 / 4.80 ( 648) link_ALPHA1-2 : bond 0.00650 / 0.32 ( 2) link_ALPHA1-2 : angle 1.22493 / 0.65 ( 6) link_ALPHA1-3 : bond 0.00604 / 0.27 ( 3) link_ALPHA1-3 : angle 1.70498 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00459 / 0.22 ( 5) link_ALPHA1-6 : angle 1.70882 / 0.91 ( 15) link_BETA1-4 : bond 0.00836 / 0.33 ( 8) link_BETA1-4 : angle 2.16168 / 1.30 ( 24) link_NAG-ASN : bond 0.00797 / 0.36 ( 3) link_NAG-ASN : angle 3.51485 / 1.45 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2461.21 seconds wall clock time: 43 minutes 44.61 seconds (2624.61 seconds total)