Starting phenix.real_space_refine on Wed Sep 17 23:35:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mt2_48598/09_2025/9mt2_48598.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mt2_48598/09_2025/9mt2_48598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mt2_48598/09_2025/9mt2_48598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mt2_48598/09_2025/9mt2_48598.map" model { file = "/net/cci-nas-00/data/ceres_data/9mt2_48598/09_2025/9mt2_48598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mt2_48598/09_2025/9mt2_48598.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 96 5.16 5 C 7575 2.51 5 N 1992 2.21 5 O 2202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11871 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "B" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1585 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain: "C" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1774 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "E" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1585 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain: "F" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1774 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "H" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1585 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain: "I" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1774 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3630 SG CYS C 478 30.296 70.917 13.003 1.00187.35 S ATOM 3647 SG CYS C 480 32.069 74.231 11.961 1.00197.32 S ATOM 8020 SG CYS G 57 33.653 71.941 14.588 1.00161.44 S ATOM 3542 SG CYS C 466 37.123 60.102 11.421 1.00189.33 S ATOM 434 SG CYS A 57 79.483 43.834 13.766 1.00182.52 S ATOM 7423 SG CYS F 478 79.961 47.278 15.391 1.00214.59 S ATOM 7440 SG CYS F 480 80.924 46.755 11.734 1.00213.46 S ATOM 7335 SG CYS F 466 67.384 47.515 11.955 1.00209.17 S ATOM 4227 SG CYS D 57 32.262 20.047 13.302 1.00160.49 S ATOM 11216 SG CYS I 478 34.488 16.918 13.021 1.00188.38 S ATOM 11233 SG CYS I 480 30.734 16.821 11.974 1.00185.55 S ATOM 11128 SG CYS I 466 41.107 28.292 12.154 1.00196.80 S Time building chain proxies: 2.65, per 1000 atoms: 0.22 Number of scatterers: 11871 At special positions: 0 Unit cell: (94.17, 93.44, 150.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 96 16.00 O 2202 8.00 N 1992 7.00 C 7575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 304 " - pdb=" SG CYS C 313 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 388 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 207 " - pdb=" SG CYS E 213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 220 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS F 282 " - pdb=" SG CYS F 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 313 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 388 " distance=2.03 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 237 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 207 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 220 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS I 282 " - pdb=" SG CYS I 295 " distance=2.03 Simple disulfide: pdb=" SG CYS I 304 " - pdb=" SG CYS I 313 " distance=2.03 Simple disulfide: pdb=" SG CYS I 367 " - pdb=" SG CYS I 388 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG B 301 " - " ASN B 166 " " NAG B 302 " - " ASN B 95 " " NAG C 501 " - " ASN C 398 " " NAG C 502 " - " ASN C 393 " " NAG E 301 " - " ASN E 95 " " NAG E 302 " - " ASN E 166 " " NAG F 501 " - " ASN F 398 " " NAG F 502 " - " ASN F 393 " " NAG H 301 " - " ASN H 95 " " NAG H 302 " - " ASN H 166 " " NAG I 501 " - " ASN I 398 " " NAG I 502 " - " ASN I 393 " " NAG J 1 " - " ASN C 376 " " NAG K 1 " - " ASN C 368 " " NAG L 1 " - " ASN F 376 " " NAG M 1 " - " ASN F 368 " " NAG N 1 " - " ASN I 376 " " NAG O 1 " - " ASN I 368 " " NAG S 1 " - " ASN B 178 " " NAG T 1 " - " ASN E 178 " " NAG V 1 " - " ASN H 178 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 540.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" ND1 HIS C 470 " pdb="ZN ZN C 503 " - pdb=" SG CYS G 57 " pdb="ZN ZN C 503 " - pdb=" SG CYS C 480 " pdb="ZN ZN C 503 " - pdb=" SG CYS C 478 " pdb=" ZN C 504 " pdb="ZN ZN C 504 " - pdb=" NE2 HIS C 496 " pdb="ZN ZN C 504 " - pdb=" NE2 HIS C 458 " pdb="ZN ZN C 504 " - pdb=" NE2 HIS C 460 " pdb="ZN ZN C 504 " - pdb=" SG CYS C 466 " pdb=" ZN F 503 " pdb="ZN ZN F 503 " - pdb=" ND1 HIS F 470 " pdb="ZN ZN F 503 " - pdb=" SG CYS F 480 " pdb="ZN ZN F 503 " - pdb=" SG CYS F 478 " pdb="ZN ZN F 503 " - pdb=" SG CYS A 57 " pdb=" ZN F 504 " pdb="ZN ZN F 504 " - pdb=" NE2 HIS F 458 " pdb="ZN ZN F 504 " - pdb=" NE2 HIS F 460 " pdb="ZN ZN F 504 " - pdb=" NE2 HIS F 496 " pdb="ZN ZN F 504 " - pdb=" SG CYS F 466 " pdb=" ZN I 503 " pdb="ZN ZN I 503 " - pdb=" ND1 HIS I 470 " pdb="ZN ZN I 503 " - pdb=" SG CYS D 57 " pdb="ZN ZN I 503 " - pdb=" SG CYS I 480 " pdb="ZN ZN I 503 " - pdb=" SG CYS I 478 " pdb=" ZN I 504 " pdb="ZN ZN I 504 " - pdb=" NE2 HIS I 460 " pdb="ZN ZN I 504 " - pdb=" NE2 HIS I 496 " pdb="ZN ZN I 504 " - pdb=" NE2 HIS I 458 " pdb="ZN ZN I 504 " - pdb=" SG CYS I 466 " Number of angles added : 18 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 17 sheets defined 46.4% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 17 through 41 Processing helix chain 'A' and resid 42 through 52 Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.524A pdb=" N LEU B 81 " --> pdb=" O MET B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 4.181A pdb=" N GLY B 133 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS B 135 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 187 through 200 Processing helix chain 'B' and resid 222 through 229 removed outlier: 6.555A pdb=" N ASP B 227 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 228 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS B 229 " --> pdb=" O PHE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.731A pdb=" N THR B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 297 through 303 removed outlier: 3.884A pdb=" N LYS C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 310 through 329 Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.623A pdb=" N ILE C 348 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 362 Processing helix chain 'C' and resid 402 through 429 removed outlier: 3.529A pdb=" N TRP C 406 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 408 " --> pdb=" O ASN C 404 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 454 Processing helix chain 'D' and resid 3 through 10 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 42 Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'E' and resid 77 through 84 Processing helix chain 'E' and resid 142 through 152 Processing helix chain 'E' and resid 187 through 200 removed outlier: 3.931A pdb=" N LYS E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 229 removed outlier: 7.124A pdb=" N ASP E 227 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR E 228 " --> pdb=" O SER E 225 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS E 229 " --> pdb=" O PHE E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 249 removed outlier: 3.682A pdb=" N THR E 244 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL E 249 " --> pdb=" O LEU E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 288 Processing helix chain 'F' and resid 297 through 303 Processing helix chain 'F' and resid 310 through 328 Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'F' and resid 402 through 429 removed outlier: 3.965A pdb=" N GLU F 421 " --> pdb=" O MET F 417 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 454 Processing helix chain 'G' and resid 3 through 9 Processing helix chain 'G' and resid 10 through 15 Processing helix chain 'G' and resid 17 through 41 Processing helix chain 'G' and resid 42 through 52 Processing helix chain 'H' and resid 77 through 84 removed outlier: 3.615A pdb=" N HIS H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 135 removed outlier: 4.010A pdb=" N GLY H 133 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 152 Processing helix chain 'H' and resid 187 through 200 removed outlier: 3.547A pdb=" N LYS H 191 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 229 removed outlier: 6.595A pdb=" N ASP H 227 " --> pdb=" O SER H 224 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR H 228 " --> pdb=" O SER H 225 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS H 229 " --> pdb=" O PHE H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 248 removed outlier: 3.725A pdb=" N THR H 244 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 288 Processing helix chain 'I' and resid 297 through 303 Processing helix chain 'I' and resid 310 through 328 removed outlier: 3.519A pdb=" N ASP I 314 " --> pdb=" O SER I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 347 removed outlier: 3.914A pdb=" N GLN I 342 " --> pdb=" O ASN I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 362 Processing helix chain 'I' and resid 402 through 429 removed outlier: 3.924A pdb=" N GLU I 421 " --> pdb=" O MET I 417 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR I 422 " --> pdb=" O LEU I 418 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 454 Processing sheet with id=AA1, first strand: chain 'B' and resid 68 through 74 Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 93 Processing sheet with id=AA3, first strand: chain 'C' and resid 281 through 283 Processing sheet with id=AA4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA5, first strand: chain 'C' and resid 458 through 461 removed outlier: 3.908A pdb=" N HIS C 458 " --> pdb=" O HIS C 493 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS C 493 " --> pdb=" O HIS C 458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 62 through 63 removed outlier: 3.597A pdb=" N PHE E 62 " --> pdb=" O PHE E 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 90 through 93 Processing sheet with id=AA8, first strand: chain 'E' and resid 125 through 126 removed outlier: 3.831A pdb=" N MET E 162 " --> pdb=" O ILE E 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 281 through 283 Processing sheet with id=AB1, first strand: chain 'F' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'F' and resid 458 through 461 removed outlier: 3.767A pdb=" N HIS F 458 " --> pdb=" O HIS F 493 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 62 through 63 removed outlier: 3.609A pdb=" N PHE H 62 " --> pdb=" O PHE H 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 90 through 93 Processing sheet with id=AB5, first strand: chain 'H' and resid 125 through 126 removed outlier: 3.669A pdb=" N MET H 162 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 281 through 283 Processing sheet with id=AB7, first strand: chain 'I' and resid 391 through 392 Processing sheet with id=AB8, first strand: chain 'I' and resid 458 through 461 removed outlier: 3.762A pdb=" N HIS I 458 " --> pdb=" O HIS I 493 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1485 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: 1.72 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3673 1.34 - 1.46: 2559 1.46 - 1.58: 5780 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 12147 Sorted by residual: bond pdb=" N ASN E 95 " pdb=" CA ASN E 95 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.02e-02 9.61e+03 1.00e+01 bond pdb=" N ILE C 391 " pdb=" CA ILE C 391 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.55e+00 bond pdb=" N HIS E 233 " pdb=" CA HIS E 233 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.19e-02 7.06e+03 8.32e+00 bond pdb=" N ASN B 232 " pdb=" CA ASN B 232 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.73e+00 bond pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.22e-02 6.72e+03 7.62e+00 ... (remaining 12142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 16023 1.76 - 3.52: 355 3.52 - 5.28: 25 5.28 - 7.04: 5 7.04 - 8.80: 2 Bond angle restraints: 16410 Sorted by residual: angle pdb=" N ILE H 64 " pdb=" CA ILE H 64 " pdb=" C ILE H 64 " ideal model delta sigma weight residual 112.96 109.39 3.57 1.00e+00 1.00e+00 1.27e+01 angle pdb=" CA ASP E 240 " pdb=" CB ASP E 240 " pdb=" CG ASP E 240 " ideal model delta sigma weight residual 112.60 116.02 -3.42 1.00e+00 1.00e+00 1.17e+01 angle pdb=" CA THR E 76 " pdb=" CB THR E 76 " pdb=" OG1 THR E 76 " ideal model delta sigma weight residual 109.60 104.91 4.69 1.50e+00 4.44e-01 9.77e+00 angle pdb=" O ASN E 232 " pdb=" C ASN E 232 " pdb=" N HIS E 233 " ideal model delta sigma weight residual 120.58 124.06 -3.48 1.13e+00 7.83e-01 9.47e+00 angle pdb=" CA HIS H 233 " pdb=" C HIS H 233 " pdb=" O HIS H 233 " ideal model delta sigma weight residual 121.98 117.51 4.47 1.47e+00 4.63e-01 9.27e+00 ... (remaining 16405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 7134 18.05 - 36.10: 470 36.10 - 54.14: 80 54.14 - 72.19: 26 72.19 - 90.24: 6 Dihedral angle restraints: 7716 sinusoidal: 3609 harmonic: 4107 Sorted by residual: dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual -86.00 -152.73 66.73 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS B 213 " pdb=" CB CYS B 213 " ideal model delta sinusoidal sigma weight residual -86.00 -41.97 -44.03 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS E 220 " pdb=" SG CYS E 220 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual -86.00 -42.80 -43.20 1 1.00e+01 1.00e-02 2.60e+01 ... (remaining 7713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1861 0.117 - 0.233: 29 0.233 - 0.350: 2 0.350 - 0.467: 0 0.467 - 0.583: 1 Chirality restraints: 1893 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.31e+02 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.56e+01 chirality pdb=" C1 NAG H 302 " pdb=" ND2 ASN H 166 " pdb=" C2 NAG H 302 " pdb=" O5 NAG H 302 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.51e+00 ... (remaining 1890 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 2 " 0.336 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG V 2 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG V 2 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG V 2 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG V 2 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 95 " -0.041 2.00e-02 2.50e+03 2.66e-01 8.83e+02 pdb=" CG ASN H 95 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN H 95 " -0.190 2.00e-02 2.50e+03 pdb=" ND2 ASN H 95 " 0.464 2.00e-02 2.50e+03 pdb=" C1 NAG H 301 " -0.307 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 393 " 0.174 2.00e-02 2.50e+03 2.18e-01 5.94e+02 pdb=" CG ASN C 393 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C 393 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 393 " -0.365 2.00e-02 2.50e+03 pdb=" C1 NAG C 502 " 0.262 2.00e-02 2.50e+03 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 192 2.68 - 3.23: 11258 3.23 - 3.79: 18408 3.79 - 4.34: 24525 4.34 - 4.90: 40499 Nonbonded interactions: 94882 Sorted by model distance: nonbonded pdb=" OG SER I 349 " pdb=" OD1 ASN I 351 " model vdw 2.123 3.040 nonbonded pdb=" OG SER H 97 " pdb=" O VAL H 112 " model vdw 2.209 3.040 nonbonded pdb=" O SER B 173 " pdb=" OD1 ASN B 218 " model vdw 2.231 3.040 nonbonded pdb=" NE2 GLN B 219 " pdb=" OD1 ASP B 222 " model vdw 2.288 3.120 nonbonded pdb=" O ALA G 33 " pdb=" ND2 ASN G 37 " model vdw 2.298 3.120 ... (remaining 94877 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' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.250 Find NCS groups from input model: 0.270 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:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 0.298 12228 Z= 0.254 Angle : 0.683 35.820 16578 Z= 0.341 Chirality : 0.044 0.583 1893 Planarity : 0.009 0.291 2022 Dihedral : 12.224 90.238 4995 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.08 % Allowed : 0.71 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.87 (0.24), residues: 1392 helix: 1.71 (0.23), residues: 582 sheet: 0.75 (0.61), residues: 96 loop : -0.38 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 79 TYR 0.011 0.001 TYR C 396 PHE 0.011 0.001 PHE E 239 TRP 0.011 0.001 TRP E 156 HIS 0.006 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00343 (12147) covalent geometry : angle 0.56854 (16410) SS BOND : bond 0.00109 ( 21) SS BOND : angle 0.80549 ( 42) hydrogen bonds : bond 0.17664 ( 534) hydrogen bonds : angle 5.99971 ( 1485) metal coordination : bond 0.09246 ( 24) metal coordination : angle 9.86813 ( 18) link_BETA1-4 : bond 0.01808 ( 15) link_BETA1-4 : angle 2.57026 ( 45) link_NAG-ASN : bond 0.00351 ( 21) link_NAG-ASN : angle 2.34731 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.6075 (ptp) cc_final: 0.5577 (ppp) REVERT: C 294 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7809 (ttmp) REVERT: C 397 LEU cc_start: 0.8421 (mp) cc_final: 0.8215 (mt) REVERT: E 84 HIS cc_start: 0.6598 (t-90) cc_final: 0.6177 (t-90) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.4627 time to fit residues: 98.1566 Evaluate side-chains 182 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 391 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0020 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN E 106 ASN E 219 GLN E 254 HIS H 84 HIS H 176 GLN ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.201415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.166658 restraints weight = 15940.850| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.38 r_work: 0.3797 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12228 Z= 0.120 Angle : 0.593 8.505 16578 Z= 0.292 Chirality : 0.040 0.223 1893 Planarity : 0.004 0.034 2022 Dihedral : 6.998 65.431 2255 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.03 % Allowed : 7.13 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.88 (0.24), residues: 1392 helix: 1.67 (0.22), residues: 600 sheet: 0.28 (0.50), residues: 126 loop : -0.33 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 425 TYR 0.013 0.001 TYR E 100 PHE 0.017 0.001 PHE H 247 TRP 0.025 0.001 TRP I 406 HIS 0.005 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00253 (12147) covalent geometry : angle 0.56261 (16410) SS BOND : bond 0.00277 ( 21) SS BOND : angle 1.43168 ( 42) hydrogen bonds : bond 0.04779 ( 534) hydrogen bonds : angle 4.76127 ( 1485) metal coordination : bond 0.01414 ( 24) metal coordination : angle 2.46006 ( 18) link_BETA1-4 : bond 0.00387 ( 15) link_BETA1-4 : angle 1.82403 ( 45) link_NAG-ASN : bond 0.00224 ( 21) link_NAG-ASN : angle 2.14543 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.6136 (ptp) cc_final: 0.5639 (ppp) REVERT: C 294 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7954 (ttmp) REVERT: C 397 LEU cc_start: 0.8507 (mp) cc_final: 0.8223 (mt) REVERT: F 293 MET cc_start: 0.7444 (tmm) cc_final: 0.7092 (tmm) REVERT: H 119 MET cc_start: 0.5946 (ptt) cc_final: 0.5740 (ptt) REVERT: I 399 THR cc_start: 0.8087 (m) cc_final: 0.7817 (m) REVERT: I 429 THR cc_start: 0.8354 (m) cc_final: 0.8135 (m) outliers start: 13 outliers final: 6 residues processed: 168 average time/residue: 0.5106 time to fit residues: 93.8596 Evaluate side-chains 161 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 97 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 9 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN E 96 ASN ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN H 243 ASN I 342 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.196953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.161054 restraints weight = 15902.932| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.43 r_work: 0.3747 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12228 Z= 0.185 Angle : 0.607 9.913 16578 Z= 0.299 Chirality : 0.041 0.208 1893 Planarity : 0.004 0.036 2022 Dihedral : 6.354 54.694 2253 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.82 % Allowed : 8.31 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.66 (0.23), residues: 1392 helix: 1.28 (0.21), residues: 606 sheet: 0.36 (0.49), residues: 126 loop : -0.27 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 425 TYR 0.015 0.001 TYR C 396 PHE 0.023 0.002 PHE H 247 TRP 0.033 0.002 TRP I 406 HIS 0.010 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00428 (12147) covalent geometry : angle 0.58047 (16410) SS BOND : bond 0.00558 ( 21) SS BOND : angle 1.21216 ( 42) hydrogen bonds : bond 0.04334 ( 534) hydrogen bonds : angle 4.52305 ( 1485) metal coordination : bond 0.01017 ( 24) metal coordination : angle 1.56520 ( 18) link_BETA1-4 : bond 0.00532 ( 15) link_BETA1-4 : angle 1.85331 ( 45) link_NAG-ASN : bond 0.00541 ( 21) link_NAG-ASN : angle 2.23071 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.6422 (ptp) cc_final: 0.5802 (ppp) REVERT: C 294 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7979 (ttmp) REVERT: E 72 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8253 (t) REVERT: F 293 MET cc_start: 0.7770 (tmm) cc_final: 0.7392 (tmm) REVERT: H 75 LEU cc_start: 0.8202 (mp) cc_final: 0.7890 (mt) REVERT: H 109 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7520 (tm) REVERT: I 399 THR cc_start: 0.8199 (m) cc_final: 0.7887 (m) outliers start: 23 outliers final: 10 residues processed: 177 average time/residue: 0.4868 time to fit residues: 94.4789 Evaluate side-chains 171 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 158 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 0.0270 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 64 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN E 78 GLN E 219 GLN ** H 198 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 = 0.4356 r_free = 0.4356 target = 0.195991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.160611 restraints weight = 15845.190| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.41 r_work: 0.3748 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12228 Z= 0.155 Angle : 0.573 8.193 16578 Z= 0.284 Chirality : 0.040 0.237 1893 Planarity : 0.003 0.037 2022 Dihedral : 6.094 52.785 2253 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.82 % Allowed : 10.21 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.71 (0.23), residues: 1392 helix: 1.33 (0.21), residues: 606 sheet: 0.47 (0.49), residues: 126 loop : -0.28 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 425 TYR 0.009 0.001 TYR B 99 PHE 0.022 0.001 PHE H 247 TRP 0.033 0.002 TRP I 406 HIS 0.006 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00357 (12147) covalent geometry : angle 0.54795 (16410) SS BOND : bond 0.00549 ( 21) SS BOND : angle 1.34316 ( 42) hydrogen bonds : bond 0.03956 ( 534) hydrogen bonds : angle 4.39806 ( 1485) metal coordination : bond 0.00969 ( 24) metal coordination : angle 1.47060 ( 18) link_BETA1-4 : bond 0.00435 ( 15) link_BETA1-4 : angle 1.76767 ( 45) link_NAG-ASN : bond 0.00400 ( 21) link_NAG-ASN : angle 2.03886 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.430 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: B 162 MET cc_start: 0.6529 (ptp) cc_final: 0.5754 (ppp) REVERT: C 294 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7949 (ttmp) REVERT: E 72 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8270 (t) REVERT: E 84 HIS cc_start: 0.6686 (t-90) cc_final: 0.6114 (t-90) REVERT: F 294 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8201 (ptmt) REVERT: F 322 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7676 (t0) REVERT: H 109 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7621 (tm) REVERT: I 399 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7839 (m) outliers start: 23 outliers final: 10 residues processed: 175 average time/residue: 0.4950 time to fit residues: 94.8912 Evaluate side-chains 177 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain F residue 294 LYS Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 322 ASN Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 429 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 120 optimal weight: 0.0010 chunk 105 optimal weight: 0.4980 chunk 112 optimal weight: 9.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN E 71 GLN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.195287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.159970 restraints weight = 15815.311| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.40 r_work: 0.3733 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12228 Z= 0.163 Angle : 0.576 10.226 16578 Z= 0.286 Chirality : 0.040 0.263 1893 Planarity : 0.004 0.038 2022 Dihedral : 5.894 53.551 2253 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.22 % Allowed : 11.56 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.68 (0.23), residues: 1392 helix: 1.30 (0.21), residues: 606 sheet: 0.37 (0.48), residues: 126 loop : -0.27 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 425 TYR 0.017 0.001 TYR E 99 PHE 0.022 0.001 PHE H 247 TRP 0.034 0.002 TRP I 406 HIS 0.006 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00378 (12147) covalent geometry : angle 0.55307 (16410) SS BOND : bond 0.00353 ( 21) SS BOND : angle 1.26788 ( 42) hydrogen bonds : bond 0.03896 ( 534) hydrogen bonds : angle 4.32799 ( 1485) metal coordination : bond 0.00934 ( 24) metal coordination : angle 1.40739 ( 18) link_BETA1-4 : bond 0.00426 ( 15) link_BETA1-4 : angle 1.77140 ( 45) link_NAG-ASN : bond 0.00423 ( 21) link_NAG-ASN : angle 1.96510 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.454 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: B 162 MET cc_start: 0.6536 (ptp) cc_final: 0.5829 (ppp) REVERT: C 294 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7942 (ttmp) REVERT: C 382 GLN cc_start: 0.8317 (pt0) cc_final: 0.8097 (pt0) REVERT: E 72 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8288 (t) REVERT: E 84 HIS cc_start: 0.6722 (t-90) cc_final: 0.6148 (t-90) REVERT: F 293 MET cc_start: 0.7971 (ttp) cc_final: 0.7536 (tmm) REVERT: F 294 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8215 (ptmt) REVERT: F 379 LEU cc_start: 0.8478 (mt) cc_final: 0.8202 (mp) REVERT: F 382 GLN cc_start: 0.8051 (pt0) cc_final: 0.7746 (pm20) REVERT: F 407 ILE cc_start: 0.7808 (mm) cc_final: 0.7605 (mt) REVERT: H 75 LEU cc_start: 0.8209 (mp) cc_final: 0.7874 (mt) REVERT: I 399 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7864 (m) outliers start: 28 outliers final: 15 residues processed: 191 average time/residue: 0.4851 time to fit residues: 102.0634 Evaluate side-chains 190 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 237 CYS Chi-restraints excluded: chain F residue 294 LYS Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 322 ASN Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN F 322 ASN ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 ASN H 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.193680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158159 restraints weight = 15762.784| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.41 r_work: 0.3712 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 12228 Z= 0.225 Angle : 0.622 12.210 16578 Z= 0.307 Chirality : 0.042 0.290 1893 Planarity : 0.004 0.040 2022 Dihedral : 5.964 57.029 2253 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.61 % Allowed : 12.98 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.50 (0.23), residues: 1392 helix: 1.11 (0.21), residues: 606 sheet: 0.35 (0.48), residues: 126 loop : -0.33 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 425 TYR 0.013 0.002 TYR C 396 PHE 0.025 0.002 PHE H 247 TRP 0.037 0.002 TRP I 406 HIS 0.007 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00525 (12147) covalent geometry : angle 0.59405 (16410) SS BOND : bond 0.00703 ( 21) SS BOND : angle 1.43051 ( 42) hydrogen bonds : bond 0.04122 ( 534) hydrogen bonds : angle 4.38248 ( 1485) metal coordination : bond 0.00950 ( 24) metal coordination : angle 1.45198 ( 18) link_BETA1-4 : bond 0.00506 ( 15) link_BETA1-4 : angle 1.84548 ( 45) link_NAG-ASN : bond 0.00592 ( 21) link_NAG-ASN : angle 2.31884 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.499 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: B 162 MET cc_start: 0.6622 (ptp) cc_final: 0.5852 (ppp) REVERT: C 294 LYS cc_start: 0.8326 (ttmm) cc_final: 0.7963 (ttmp) REVERT: C 382 GLN cc_start: 0.8400 (pt0) cc_final: 0.8093 (pt0) REVERT: E 72 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8291 (t) REVERT: E 84 HIS cc_start: 0.6785 (t-90) cc_final: 0.6218 (t-90) REVERT: F 371 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7961 (ttpt) REVERT: F 382 GLN cc_start: 0.8146 (pt0) cc_final: 0.7904 (pt0) REVERT: G 10 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.4550 (mp0) REVERT: I 345 ASN cc_start: 0.8232 (m-40) cc_final: 0.7969 (m110) REVERT: I 399 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7888 (m) outliers start: 33 outliers final: 17 residues processed: 184 average time/residue: 0.4864 time to fit residues: 98.3716 Evaluate side-chains 187 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 237 CYS Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 371 LYS Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 429 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 27 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 112 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 124 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN E 71 GLN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.194801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.159578 restraints weight = 15684.464| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.40 r_work: 0.3733 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 12228 Z= 0.140 Angle : 0.567 14.080 16578 Z= 0.282 Chirality : 0.040 0.288 1893 Planarity : 0.004 0.041 2022 Dihedral : 5.599 53.709 2253 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.22 % Allowed : 13.46 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.65 (0.23), residues: 1392 helix: 1.34 (0.21), residues: 603 sheet: 0.34 (0.48), residues: 126 loop : -0.35 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 425 TYR 0.010 0.001 TYR E 99 PHE 0.018 0.001 PHE H 247 TRP 0.033 0.002 TRP I 406 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00327 (12147) covalent geometry : angle 0.54553 (16410) SS BOND : bond 0.00582 ( 21) SS BOND : angle 1.33138 ( 42) hydrogen bonds : bond 0.03734 ( 534) hydrogen bonds : angle 4.23346 ( 1485) metal coordination : bond 0.00861 ( 24) metal coordination : angle 1.35306 ( 18) link_BETA1-4 : bond 0.00412 ( 15) link_BETA1-4 : angle 1.72525 ( 45) link_NAG-ASN : bond 0.00301 ( 21) link_NAG-ASN : angle 1.78778 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.437 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: B 162 MET cc_start: 0.6602 (ptp) cc_final: 0.5859 (ppp) REVERT: B 196 MET cc_start: 0.7980 (mtp) cc_final: 0.7686 (mtp) REVERT: C 294 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7970 (ttmp) REVERT: C 382 GLN cc_start: 0.8326 (pt0) cc_final: 0.8014 (pt0) REVERT: E 72 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8294 (t) REVERT: E 84 HIS cc_start: 0.6741 (t-90) cc_final: 0.6144 (t-90) REVERT: F 382 GLN cc_start: 0.8078 (pt0) cc_final: 0.7845 (pt0) REVERT: H 75 LEU cc_start: 0.8217 (mp) cc_final: 0.7878 (mt) REVERT: I 345 ASN cc_start: 0.8218 (m-40) cc_final: 0.7921 (m110) REVERT: I 399 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7876 (m) outliers start: 28 outliers final: 20 residues processed: 201 average time/residue: 0.4508 time to fit residues: 100.2726 Evaluate side-chains 200 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 237 CYS Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 322 ASN Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 429 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 126 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 84 optimal weight: 0.1980 chunk 104 optimal weight: 0.0030 chunk 25 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.1428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 HIS E 71 GLN ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.196371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.161400 restraints weight = 15859.941| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.43 r_work: 0.3756 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 12228 Z= 0.103 Angle : 0.550 12.705 16578 Z= 0.272 Chirality : 0.039 0.266 1893 Planarity : 0.003 0.046 2022 Dihedral : 5.296 53.395 2253 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.90 % Allowed : 14.01 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.87 (0.24), residues: 1392 helix: 1.59 (0.22), residues: 603 sheet: 0.50 (0.49), residues: 126 loop : -0.31 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 425 TYR 0.010 0.001 TYR I 369 PHE 0.012 0.001 PHE H 247 TRP 0.029 0.002 TRP F 406 HIS 0.003 0.001 HIS C 460 Details of bonding type rmsd covalent geometry : bond 0.00232 (12147) covalent geometry : angle 0.53122 (16410) SS BOND : bond 0.00546 ( 21) SS BOND : angle 1.26039 ( 42) hydrogen bonds : bond 0.03464 ( 534) hydrogen bonds : angle 4.06407 ( 1485) metal coordination : bond 0.00792 ( 24) metal coordination : angle 1.30783 ( 18) link_BETA1-4 : bond 0.00478 ( 15) link_BETA1-4 : angle 1.69872 ( 45) link_NAG-ASN : bond 0.00191 ( 21) link_NAG-ASN : angle 1.61711 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.336 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: B 162 MET cc_start: 0.6560 (ptp) cc_final: 0.5844 (ppp) REVERT: B 196 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7609 (ttp) REVERT: C 294 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7988 (ttmp) REVERT: C 382 GLN cc_start: 0.8231 (pt0) cc_final: 0.7940 (pt0) REVERT: E 84 HIS cc_start: 0.6646 (t-90) cc_final: 0.6098 (t-90) REVERT: E 234 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.5149 (pp) REVERT: F 428 LYS cc_start: 0.8572 (ptmm) cc_final: 0.8340 (ptmm) REVERT: H 75 LEU cc_start: 0.8173 (mp) cc_final: 0.7906 (mt) REVERT: H 152 LEU cc_start: 0.8212 (mt) cc_final: 0.7929 (mp) REVERT: I 345 ASN cc_start: 0.8233 (m-40) cc_final: 0.7948 (m110) REVERT: I 399 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7886 (m) outliers start: 24 outliers final: 13 residues processed: 183 average time/residue: 0.5078 time to fit residues: 101.4551 Evaluate side-chains 173 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 322 ASN Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 429 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 23 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 66 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 0.0370 chunk 51 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN C 322 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 GLN ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** 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 = 0.4346 r_free = 0.4346 target = 0.195112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159927 restraints weight = 15691.188| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.41 r_work: 0.3738 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12228 Z= 0.144 Angle : 0.582 12.206 16578 Z= 0.288 Chirality : 0.040 0.264 1893 Planarity : 0.004 0.046 2022 Dihedral : 5.340 53.945 2253 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.58 % Allowed : 14.81 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.80 (0.23), residues: 1392 helix: 1.48 (0.21), residues: 606 sheet: 0.45 (0.49), residues: 126 loop : -0.30 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 425 TYR 0.009 0.001 TYR F 369 PHE 0.018 0.001 PHE H 247 TRP 0.033 0.002 TRP I 406 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00336 (12147) covalent geometry : angle 0.56058 (16410) SS BOND : bond 0.00596 ( 21) SS BOND : angle 1.33510 ( 42) hydrogen bonds : bond 0.03616 ( 534) hydrogen bonds : angle 4.09977 ( 1485) metal coordination : bond 0.00786 ( 24) metal coordination : angle 1.24228 ( 18) link_BETA1-4 : bond 0.00408 ( 15) link_BETA1-4 : angle 1.73126 ( 45) link_NAG-ASN : bond 0.00333 ( 21) link_NAG-ASN : angle 1.87597 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.468 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: B 162 MET cc_start: 0.6596 (ptp) cc_final: 0.5908 (ppp) REVERT: B 196 MET cc_start: 0.7934 (mtp) cc_final: 0.7675 (mtp) REVERT: C 294 LYS cc_start: 0.8314 (ttmm) cc_final: 0.8002 (ttmp) REVERT: C 382 GLN cc_start: 0.8309 (pt0) cc_final: 0.8019 (pt0) REVERT: E 84 HIS cc_start: 0.6625 (t-90) cc_final: 0.6106 (t-90) REVERT: F 428 LYS cc_start: 0.8586 (ptmm) cc_final: 0.8377 (ptmm) REVERT: H 75 LEU cc_start: 0.8207 (mp) cc_final: 0.7934 (mt) REVERT: H 152 LEU cc_start: 0.8261 (mt) cc_final: 0.7998 (mp) REVERT: I 345 ASN cc_start: 0.8309 (m-40) cc_final: 0.8032 (m110) REVERT: I 399 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7923 (m) outliers start: 20 outliers final: 12 residues processed: 179 average time/residue: 0.4883 time to fit residues: 96.0254 Evaluate side-chains 179 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN H 106 ASN H 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.194510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159297 restraints weight = 15813.198| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.41 r_work: 0.3730 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 12228 Z= 0.160 Angle : 0.612 14.280 16578 Z= 0.301 Chirality : 0.041 0.268 1893 Planarity : 0.004 0.047 2022 Dihedral : 5.358 52.718 2253 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.11 % Allowed : 15.20 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.74 (0.23), residues: 1392 helix: 1.43 (0.21), residues: 606 sheet: 0.46 (0.49), residues: 126 loop : -0.34 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 425 TYR 0.009 0.001 TYR C 321 PHE 0.018 0.001 PHE H 247 TRP 0.034 0.002 TRP I 406 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00374 (12147) covalent geometry : angle 0.59012 (16410) SS BOND : bond 0.00664 ( 21) SS BOND : angle 1.38413 ( 42) hydrogen bonds : bond 0.03706 ( 534) hydrogen bonds : angle 4.13185 ( 1485) metal coordination : bond 0.00791 ( 24) metal coordination : angle 1.25255 ( 18) link_BETA1-4 : bond 0.00411 ( 15) link_BETA1-4 : angle 1.74527 ( 45) link_NAG-ASN : bond 0.00429 ( 21) link_NAG-ASN : angle 1.95168 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 LYS cc_start: 0.8456 (mmmm) cc_final: 0.8135 (mtpp) REVERT: B 162 MET cc_start: 0.6632 (ptp) cc_final: 0.5891 (ppp) REVERT: B 196 MET cc_start: 0.7970 (mtp) cc_final: 0.7668 (mtp) REVERT: C 294 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7985 (ttmp) REVERT: C 382 GLN cc_start: 0.8357 (pt0) cc_final: 0.8023 (pt0) REVERT: E 72 SER cc_start: 0.8531 (t) cc_final: 0.8302 (t) REVERT: E 84 HIS cc_start: 0.6668 (t-90) cc_final: 0.6137 (t-90) REVERT: F 428 LYS cc_start: 0.8577 (ptmm) cc_final: 0.8347 (ptmm) REVERT: H 152 LEU cc_start: 0.8280 (mt) cc_final: 0.8014 (mp) REVERT: I 345 ASN cc_start: 0.8322 (m-40) cc_final: 0.8049 (m110) REVERT: I 399 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7934 (m) outliers start: 14 outliers final: 11 residues processed: 171 average time/residue: 0.5086 time to fit residues: 95.3405 Evaluate side-chains 175 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN E 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.193245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.157853 restraints weight = 15747.319| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.39 r_work: 0.3712 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 12228 Z= 0.198 Angle : 0.641 14.180 16578 Z= 0.315 Chirality : 0.042 0.257 1893 Planarity : 0.004 0.049 2022 Dihedral : 5.586 53.991 2253 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.27 % Allowed : 14.96 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: 0.54 (0.23), residues: 1392 helix: 1.21 (0.21), residues: 606 sheet: 0.41 (0.49), residues: 126 loop : -0.39 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 425 TYR 0.012 0.001 TYR C 396 PHE 0.020 0.002 PHE H 247 TRP 0.037 0.002 TRP F 406 HIS 0.006 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00462 (12147) covalent geometry : angle 0.61786 (16410) SS BOND : bond 0.00677 ( 21) SS BOND : angle 1.33300 ( 42) hydrogen bonds : bond 0.03991 ( 534) hydrogen bonds : angle 4.28596 ( 1485) metal coordination : bond 0.00831 ( 24) metal coordination : angle 1.31514 ( 18) link_BETA1-4 : bond 0.00466 ( 15) link_BETA1-4 : angle 1.78332 ( 45) link_NAG-ASN : bond 0.00541 ( 21) link_NAG-ASN : angle 2.13692 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3709.52 seconds wall clock time: 64 minutes 18.08 seconds (3858.08 seconds total)