Starting phenix.real_space_refine on Wed Jul 30 09:43:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mt2_48598/07_2025/9mt2_48598.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mt2_48598/07_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_48598/07_2025/9mt2_48598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mt2_48598/07_2025/9mt2_48598.map" model { file = "/net/cci-nas-00/data/ceres_data/9mt2_48598/07_2025/9mt2_48598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mt2_48598/07_2025/9mt2_48598.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.77, per 1000 atoms: 0.82 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: 2.96 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.27 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: 3.37 Time building geometry restraints manager: 3.52 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: 7.190 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: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 33.560 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP E 156 HIS 0.006 0.001 HIS E 198 PHE 0.011 0.001 PHE E 239 TYR 0.011 0.001 TYR C 396 ARG 0.003 0.000 ARG E 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 21) link_NAG-ASN : angle 2.34731 ( 63) link_BETA1-4 : bond 0.01808 ( 15) link_BETA1-4 : angle 2.57026 ( 45) hydrogen bonds : bond 0.17664 ( 534) hydrogen bonds : angle 5.99971 ( 1485) metal coordination : bond 0.09246 ( 24) metal coordination : angle 9.86813 ( 18) SS BOND : bond 0.00109 ( 21) SS BOND : angle 0.80549 ( 42) covalent geometry : bond 0.00343 (12147) covalent geometry : angle 0.56854 (16410) *********************** 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 : 1.651 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: 0.8214 (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: 1.0324 time to fit residues: 219.7936 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 : 1.412 ------------------------------------------------------------------------------- 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 113 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 0.0970 chunk 34 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.0570 chunk 78 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 HIS H 84 HIS H 176 GLN ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.199971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165048 restraints weight = 15866.395| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.38 r_work: 0.3775 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12228 Z= 0.142 Angle : 0.611 8.539 16578 Z= 0.301 Chirality : 0.041 0.227 1893 Planarity : 0.004 0.035 2022 Dihedral : 7.057 65.007 2255 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.35 % Allowed : 6.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1392 helix: 1.56 (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 TRP 0.027 0.002 TRP I 406 HIS 0.007 0.001 HIS B 198 PHE 0.020 0.001 PHE H 247 TYR 0.013 0.001 TYR E 100 ARG 0.004 0.000 ARG I 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 21) link_NAG-ASN : angle 2.20590 ( 63) link_BETA1-4 : bond 0.00420 ( 15) link_BETA1-4 : angle 1.90783 ( 45) hydrogen bonds : bond 0.04648 ( 534) hydrogen bonds : angle 4.76229 ( 1485) metal coordination : bond 0.01245 ( 24) metal coordination : angle 2.34715 ( 18) SS BOND : bond 0.00289 ( 21) SS BOND : angle 1.33734 ( 42) covalent geometry : bond 0.00315 (12147) covalent geometry : angle 0.58074 (16410) *********************** 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 180 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.6225 (ptp) cc_final: 0.5682 (ppp) REVERT: C 294 LYS cc_start: 0.8349 (ttmm) cc_final: 0.7963 (ttmp) REVERT: C 397 LEU cc_start: 0.8604 (mp) cc_final: 0.8296 (mt) REVERT: E 72 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8223 (t) REVERT: I 399 THR cc_start: 0.8158 (m) cc_final: 0.7894 (m) REVERT: I 429 THR cc_start: 0.8378 (m) cc_final: 0.8158 (m) outliers start: 17 outliers final: 6 residues processed: 169 average time/residue: 1.1389 time to fit residues: 211.4832 Evaluate side-chains 164 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 142 SER 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 Chi-restraints excluded: chain H residue 142 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 64 optimal weight: 0.0070 chunk 48 optimal weight: 0.5980 chunk 123 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 47 optimal weight: 0.5980 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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 E 96 ASN ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.198091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.162628 restraints weight = 16036.195| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.44 r_work: 0.3775 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12228 Z= 0.135 Angle : 0.565 9.529 16578 Z= 0.279 Chirality : 0.039 0.169 1893 Planarity : 0.003 0.035 2022 Dihedral : 6.161 54.086 2253 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1392 helix: 1.57 (0.22), residues: 600 sheet: 0.41 (0.49), residues: 126 loop : -0.31 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 406 HIS 0.007 0.001 HIS B 198 PHE 0.019 0.001 PHE H 247 TYR 0.012 0.001 TYR C 396 ARG 0.003 0.000 ARG I 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 21) link_NAG-ASN : angle 1.97649 ( 63) link_BETA1-4 : bond 0.00390 ( 15) link_BETA1-4 : angle 1.71191 ( 45) hydrogen bonds : bond 0.04015 ( 534) hydrogen bonds : angle 4.41940 ( 1485) metal coordination : bond 0.00970 ( 24) metal coordination : angle 1.57692 ( 18) SS BOND : bond 0.00522 ( 21) SS BOND : angle 1.05115 ( 42) covalent geometry : bond 0.00303 (12147) covalent geometry : angle 0.54177 (16410) *********************** 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 190 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.324 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: 0.6357 (ptp) cc_final: 0.5705 (ppp) REVERT: C 294 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7918 (ttmp) REVERT: E 72 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8256 (t) REVERT: F 293 MET cc_start: 0.7708 (tmm) cc_final: 0.7311 (tmm) REVERT: H 75 LEU cc_start: 0.8196 (mp) cc_final: 0.7889 (mt) REVERT: H 109 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7556 (tm) REVERT: I 303 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7895 (mtmm) REVERT: I 399 THR cc_start: 0.8170 (m) cc_final: 0.7848 (m) REVERT: I 429 THR cc_start: 0.8381 (m) cc_final: 0.8169 (m) outliers start: 23 outliers final: 10 residues processed: 176 average time/residue: 1.1473 time to fit residues: 221.7005 Evaluate side-chains 174 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 B residue 196 MET Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 50 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 118 optimal weight: 0.3980 chunk 1 optimal weight: 0.1980 chunk 111 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN E 78 GLN E 219 GLN ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.196626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.161195 restraints weight = 15841.824| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.41 r_work: 0.3752 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 12228 Z= 0.159 Angle : 0.568 8.398 16578 Z= 0.281 Chirality : 0.040 0.239 1893 Planarity : 0.003 0.037 2022 Dihedral : 6.063 52.956 2253 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.58 % Allowed : 10.06 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1392 helix: 1.42 (0.21), residues: 606 sheet: 0.43 (0.48), residues: 126 loop : -0.26 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 406 HIS 0.006 0.001 HIS B 198 PHE 0.021 0.001 PHE H 247 TYR 0.012 0.001 TYR E 99 ARG 0.004 0.000 ARG I 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 21) link_NAG-ASN : angle 2.01772 ( 63) link_BETA1-4 : bond 0.00410 ( 15) link_BETA1-4 : angle 1.77461 ( 45) hydrogen bonds : bond 0.03901 ( 534) hydrogen bonds : angle 4.36566 ( 1485) metal coordination : bond 0.00949 ( 24) metal coordination : angle 1.44747 ( 18) SS BOND : bond 0.00613 ( 21) SS BOND : angle 1.06510 ( 42) covalent geometry : bond 0.00366 (12147) covalent geometry : angle 0.54419 (16410) *********************** 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 184 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.141 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: 0.6486 (ptp) cc_final: 0.5721 (ppp) REVERT: C 294 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7940 (ttmp) REVERT: E 72 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8273 (t) REVERT: F 382 GLN cc_start: 0.8008 (pt0) cc_final: 0.7778 (pm20) REVERT: H 109 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7646 (tm) REVERT: I 303 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7932 (mtmm) REVERT: I 399 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7842 (m) REVERT: I 429 THR cc_start: 0.8365 (m) cc_final: 0.8162 (m) outliers start: 20 outliers final: 8 residues processed: 171 average time/residue: 1.5741 time to fit residues: 293.3287 Evaluate side-chains 172 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 2.869 ------------------------------------------------------------------------------- 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 298 ASN 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 Chi-restraints excluded: chain I residue 399 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 87 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 0.1980 chunk 117 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.195654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.160201 restraints weight = 15696.085| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.39 r_work: 0.3729 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 12228 Z= 0.187 Angle : 0.586 9.437 16578 Z= 0.290 Chirality : 0.041 0.255 1893 Planarity : 0.003 0.039 2022 Dihedral : 5.925 53.999 2253 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.74 % Allowed : 11.88 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.23), residues: 1392 helix: 1.27 (0.21), residues: 606 sheet: 0.40 (0.48), residues: 126 loop : -0.30 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 406 HIS 0.006 0.001 HIS B 198 PHE 0.023 0.002 PHE H 247 TYR 0.012 0.001 TYR C 396 ARG 0.005 0.000 ARG I 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 21) link_NAG-ASN : angle 2.02923 ( 63) link_BETA1-4 : bond 0.00456 ( 15) link_BETA1-4 : angle 1.79044 ( 45) hydrogen bonds : bond 0.03997 ( 534) hydrogen bonds : angle 4.36295 ( 1485) metal coordination : bond 0.00949 ( 24) metal coordination : angle 1.41300 ( 18) SS BOND : bond 0.00388 ( 21) SS BOND : angle 1.21973 ( 42) covalent geometry : bond 0.00436 (12147) covalent geometry : angle 0.56264 (16410) *********************** 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 196 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.183 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: 0.6571 (ptp) cc_final: 0.5814 (ppp) REVERT: C 294 LYS cc_start: 0.8327 (ttmm) cc_final: 0.7953 (ttmp) REVERT: C 382 GLN cc_start: 0.8342 (pt0) cc_final: 0.8091 (pt0) REVERT: E 72 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8280 (t) REVERT: E 84 HIS cc_start: 0.6752 (t-90) cc_final: 0.6179 (t-90) REVERT: F 293 MET cc_start: 0.7948 (ttp) cc_final: 0.7529 (tmm) REVERT: F 379 LEU cc_start: 0.8458 (mt) cc_final: 0.8165 (mp) REVERT: F 382 GLN cc_start: 0.8143 (pt0) cc_final: 0.7876 (pt0) REVERT: G 10 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.4492 (mp0) REVERT: H 75 LEU cc_start: 0.8198 (mp) cc_final: 0.7853 (mt) REVERT: I 345 ASN cc_start: 0.8163 (m-40) cc_final: 0.7916 (m110) REVERT: I 399 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7856 (m) outliers start: 22 outliers final: 12 residues processed: 185 average time/residue: 1.1603 time to fit residues: 236.0868 Evaluate side-chains 184 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 E residue 72 SER Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 80 LEU 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 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 142 SER Chi-restraints excluded: chain I residue 399 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 126 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 129 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 HIS H 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.195480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.160213 restraints weight = 15836.761| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.40 r_work: 0.3734 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 12228 Z= 0.167 Angle : 0.579 12.468 16578 Z= 0.287 Chirality : 0.040 0.286 1893 Planarity : 0.003 0.038 2022 Dihedral : 5.716 52.911 2253 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.22 % Allowed : 12.59 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1392 helix: 1.29 (0.21), residues: 603 sheet: 0.42 (0.48), residues: 126 loop : -0.34 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 406 HIS 0.005 0.001 HIS B 198 PHE 0.020 0.001 PHE H 247 TYR 0.013 0.001 TYR E 99 ARG 0.004 0.000 ARG I 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 21) link_NAG-ASN : angle 1.92486 ( 63) link_BETA1-4 : bond 0.00401 ( 15) link_BETA1-4 : angle 1.76026 ( 45) hydrogen bonds : bond 0.03864 ( 534) hydrogen bonds : angle 4.28689 ( 1485) metal coordination : bond 0.00893 ( 24) metal coordination : angle 1.34986 ( 18) SS BOND : bond 0.00795 ( 21) SS BOND : angle 1.48381 ( 42) covalent geometry : bond 0.00389 (12147) covalent geometry : angle 0.55491 (16410) *********************** 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 206 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 1.535 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: 0.6611 (ptp) cc_final: 0.5851 (ppp) REVERT: B 196 MET cc_start: 0.8024 (mtp) cc_final: 0.7722 (mtp) REVERT: C 294 LYS cc_start: 0.8307 (ttmm) cc_final: 0.7950 (ttmp) REVERT: C 382 GLN cc_start: 0.8359 (pt0) cc_final: 0.8084 (pt0) REVERT: E 72 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8290 (t) REVERT: E 84 HIS cc_start: 0.6752 (t-90) cc_final: 0.6169 (t-90) REVERT: F 379 LEU cc_start: 0.8461 (mt) cc_final: 0.8166 (mp) REVERT: F 382 GLN cc_start: 0.8152 (pt0) cc_final: 0.7889 (pt0) REVERT: I 345 ASN cc_start: 0.8200 (m-40) cc_final: 0.7940 (m110) REVERT: I 399 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7868 (m) outliers start: 28 outliers final: 15 residues processed: 191 average time/residue: 1.4035 time to fit residues: 295.4681 Evaluate side-chains 187 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 124 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 E residue 237 CYS Chi-restraints excluded: chain F residue 298 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 63 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain I residue 399 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 82 optimal weight: 0.4980 chunk 8 optimal weight: 0.0870 chunk 126 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 54 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.195778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.160527 restraints weight = 15871.759| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.42 r_work: 0.3741 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 12228 Z= 0.126 Angle : 0.557 13.806 16578 Z= 0.278 Chirality : 0.039 0.266 1893 Planarity : 0.003 0.041 2022 Dihedral : 5.452 52.776 2253 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.35 % Allowed : 14.09 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1392 helix: 1.48 (0.21), residues: 603 sheet: 0.43 (0.49), residues: 126 loop : -0.31 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 406 HIS 0.003 0.001 HIS B 198 PHE 0.015 0.001 PHE H 247 TYR 0.012 0.001 TYR E 99 ARG 0.003 0.000 ARG I 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 21) link_NAG-ASN : angle 1.84476 ( 63) link_BETA1-4 : bond 0.00415 ( 15) link_BETA1-4 : angle 1.71649 ( 45) hydrogen bonds : bond 0.03649 ( 534) hydrogen bonds : angle 4.14975 ( 1485) metal coordination : bond 0.00824 ( 24) metal coordination : angle 1.28871 ( 18) SS BOND : bond 0.00601 ( 21) SS BOND : angle 1.31187 ( 42) covalent geometry : bond 0.00291 (12147) covalent geometry : angle 0.53521 (16410) *********************** 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 192 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 2.040 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: 0.6592 (ptp) cc_final: 0.5875 (ppp) REVERT: B 196 MET cc_start: 0.7953 (mtp) cc_final: 0.7672 (mtp) REVERT: C 294 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7994 (ttmp) REVERT: C 382 GLN cc_start: 0.8302 (pt0) cc_final: 0.8053 (pt0) REVERT: E 72 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8288 (t) REVERT: E 84 HIS cc_start: 0.6686 (t-90) cc_final: 0.6131 (t-90) REVERT: F 293 MET cc_start: 0.7907 (ttp) cc_final: 0.7407 (tmm) REVERT: F 379 LEU cc_start: 0.8475 (mt) cc_final: 0.8183 (mp) REVERT: F 382 GLN cc_start: 0.8093 (pt0) cc_final: 0.7838 (pt0) REVERT: H 75 LEU cc_start: 0.8217 (mp) cc_final: 0.7898 (mt) REVERT: H 152 LEU cc_start: 0.8253 (mt) cc_final: 0.7974 (mp) REVERT: I 345 ASN cc_start: 0.8218 (m-40) cc_final: 0.7947 (m110) REVERT: I 399 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7883 (m) outliers start: 17 outliers final: 12 residues processed: 186 average time/residue: 1.2663 time to fit residues: 259.7503 Evaluate side-chains 188 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 237 CYS Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 337 ILE 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 247 PHE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain I residue 399 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 85 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.194584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159373 restraints weight = 15832.534| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.40 r_work: 0.3731 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12228 Z= 0.165 Angle : 0.585 12.676 16578 Z= 0.289 Chirality : 0.041 0.280 1893 Planarity : 0.003 0.044 2022 Dihedral : 5.499 53.935 2253 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.30 % Allowed : 13.06 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1392 helix: 1.39 (0.21), residues: 603 sheet: 0.42 (0.49), residues: 126 loop : -0.33 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 406 HIS 0.005 0.001 HIS B 198 PHE 0.017 0.001 PHE H 247 TYR 0.011 0.001 TYR E 99 ARG 0.004 0.000 ARG I 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 21) link_NAG-ASN : angle 1.98392 ( 63) link_BETA1-4 : bond 0.00446 ( 15) link_BETA1-4 : angle 1.77024 ( 45) hydrogen bonds : bond 0.03806 ( 534) hydrogen bonds : angle 4.20841 ( 1485) metal coordination : bond 0.00817 ( 24) metal coordination : angle 1.27525 ( 18) SS BOND : bond 0.00583 ( 21) SS BOND : angle 1.29696 ( 42) covalent geometry : bond 0.00385 (12147) covalent geometry : angle 0.56221 (16410) *********************** 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 199 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.257 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: 0.6660 (ptp) cc_final: 0.5889 (ppp) REVERT: C 294 LYS cc_start: 0.8317 (ttmm) cc_final: 0.7997 (ttmp) REVERT: C 382 GLN cc_start: 0.8361 (pt0) cc_final: 0.8070 (pt0) REVERT: E 72 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8291 (t) REVERT: E 84 HIS cc_start: 0.6677 (t-90) cc_final: 0.6164 (t-90) REVERT: F 382 GLN cc_start: 0.8154 (pt0) cc_final: 0.7899 (pt0) REVERT: H 152 LEU cc_start: 0.8279 (mt) cc_final: 0.7998 (mp) REVERT: I 345 ASN cc_start: 0.8291 (m-40) cc_final: 0.8004 (m110) REVERT: I 399 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7896 (m) outliers start: 29 outliers final: 16 residues processed: 185 average time/residue: 1.1690 time to fit residues: 236.6821 Evaluate side-chains 184 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 124 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 E residue 85 SER Chi-restraints excluded: chain E residue 237 CYS Chi-restraints excluded: chain F residue 337 ILE 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 63 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain I residue 399 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 112 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 0.0470 chunk 81 optimal weight: 0.0980 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.195621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.160555 restraints weight = 15812.902| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.40 r_work: 0.3737 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12228 Z= 0.134 Angle : 0.575 12.319 16578 Z= 0.285 Chirality : 0.040 0.261 1893 Planarity : 0.003 0.043 2022 Dihedral : 5.373 55.088 2253 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.58 % Allowed : 14.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1392 helix: 1.48 (0.21), residues: 603 sheet: 0.45 (0.49), residues: 126 loop : -0.34 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 406 HIS 0.004 0.001 HIS B 154 PHE 0.014 0.001 PHE E 70 TYR 0.013 0.001 TYR E 99 ARG 0.003 0.000 ARG I 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 21) link_NAG-ASN : angle 1.77222 ( 63) link_BETA1-4 : bond 0.00410 ( 15) link_BETA1-4 : angle 1.71378 ( 45) hydrogen bonds : bond 0.03665 ( 534) hydrogen bonds : angle 4.12024 ( 1485) metal coordination : bond 0.00791 ( 24) metal coordination : angle 1.24760 ( 18) SS BOND : bond 0.00544 ( 21) SS BOND : angle 1.22026 ( 42) covalent geometry : bond 0.00309 (12147) covalent geometry : angle 0.55573 (16410) *********************** 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 181 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.385 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: 0.6612 (ptp) cc_final: 0.5849 (ppp) REVERT: B 196 MET cc_start: 0.7975 (mtp) cc_final: 0.7729 (mtp) REVERT: C 294 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7965 (ttmp) REVERT: C 382 GLN cc_start: 0.8348 (pt0) cc_final: 0.8063 (pt0) REVERT: E 72 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8295 (t) REVERT: E 84 HIS cc_start: 0.6690 (t-90) cc_final: 0.6130 (t-90) REVERT: F 382 GLN cc_start: 0.8131 (pt0) cc_final: 0.7879 (pt0) REVERT: H 75 LEU cc_start: 0.8216 (mp) cc_final: 0.7901 (mt) REVERT: H 112 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7848 (m) REVERT: H 152 LEU cc_start: 0.8258 (mt) cc_final: 0.7969 (mp) REVERT: I 345 ASN cc_start: 0.8282 (m-40) cc_final: 0.7992 (m110) REVERT: I 399 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7899 (m) outliers start: 20 outliers final: 13 residues processed: 174 average time/residue: 1.4138 time to fit residues: 268.8463 Evaluate side-chains 175 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 237 CYS Chi-restraints excluded: chain F residue 337 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 112 VAL Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain I residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 115 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 41 optimal weight: 0.0970 chunk 27 optimal weight: 0.0980 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.195707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.160847 restraints weight = 15800.309| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.38 r_work: 0.3749 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12228 Z= 0.123 Angle : 0.573 14.220 16578 Z= 0.282 Chirality : 0.039 0.253 1893 Planarity : 0.003 0.043 2022 Dihedral : 5.196 53.687 2253 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.50 % Allowed : 14.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1392 helix: 1.61 (0.22), residues: 603 sheet: 0.42 (0.49), residues: 126 loop : -0.32 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 406 HIS 0.003 0.001 HIS B 154 PHE 0.013 0.001 PHE E 70 TYR 0.012 0.001 TYR E 99 ARG 0.002 0.000 ARG I 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 21) link_NAG-ASN : angle 1.64330 ( 63) link_BETA1-4 : bond 0.00429 ( 15) link_BETA1-4 : angle 1.71130 ( 45) hydrogen bonds : bond 0.03557 ( 534) hydrogen bonds : angle 4.05093 ( 1485) metal coordination : bond 0.00767 ( 24) metal coordination : angle 1.23939 ( 18) SS BOND : bond 0.00608 ( 21) SS BOND : angle 1.20340 ( 42) covalent geometry : bond 0.00283 (12147) covalent geometry : angle 0.55445 (16410) ********************** 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 192 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.145 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: 0.6626 (ptp) cc_final: 0.5822 (ppp) REVERT: B 196 MET cc_start: 0.7933 (mtp) cc_final: 0.7698 (mtp) REVERT: C 294 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7965 (ttmp) REVERT: C 382 GLN cc_start: 0.8302 (pt0) cc_final: 0.8053 (pt0) REVERT: E 84 HIS cc_start: 0.6651 (t-90) cc_final: 0.6108 (t-90) REVERT: F 382 GLN cc_start: 0.8105 (pt0) cc_final: 0.7868 (pt0) REVERT: H 75 LEU cc_start: 0.8199 (mp) cc_final: 0.7883 (mt) REVERT: H 112 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7839 (m) REVERT: I 345 ASN cc_start: 0.8278 (m-40) cc_final: 0.7960 (m110) REVERT: I 399 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7897 (m) outliers start: 19 outliers final: 12 residues processed: 185 average time/residue: 1.2595 time to fit residues: 256.3539 Evaluate side-chains 181 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 237 CYS Chi-restraints excluded: chain F residue 337 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 112 VAL Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain I residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 112 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 105 optimal weight: 0.0050 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.193461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158288 restraints weight = 15752.633| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.41 r_work: 0.3721 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 12228 Z= 0.188 Angle : 0.628 14.846 16578 Z= 0.305 Chirality : 0.042 0.259 1893 Planarity : 0.004 0.046 2022 Dihedral : 5.418 54.423 2253 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.50 % Allowed : 14.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1392 helix: 1.34 (0.21), residues: 606 sheet: 0.44 (0.49), residues: 126 loop : -0.34 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP I 406 HIS 0.006 0.001 HIS B 198 PHE 0.016 0.002 PHE E 70 TYR 0.026 0.002 TYR E 99 ARG 0.005 0.000 ARG I 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 21) link_NAG-ASN : angle 1.98886 ( 63) link_BETA1-4 : bond 0.00461 ( 15) link_BETA1-4 : angle 1.78742 ( 45) hydrogen bonds : bond 0.03852 ( 534) hydrogen bonds : angle 4.19238 ( 1485) metal coordination : bond 0.00793 ( 24) metal coordination : angle 1.26337 ( 18) SS BOND : bond 0.00643 ( 21) SS BOND : angle 1.26161 ( 42) covalent geometry : bond 0.00438 (12147) covalent geometry : angle 0.60752 (16410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8415.48 seconds wall clock time: 152 minutes 16.34 seconds (9136.34 seconds total)