Starting phenix.real_space_refine on Fri Oct 30 13:35:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7koo_22979/10_2026/7koo_22979_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7koo_22979/10_2026/7koo_22979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7koo_22979/10_2026/7koo_22979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7koo_22979/10_2026/7koo_22979.map" model { file = "/net/cci-nas-00/data/ceres_data/7koo_22979/10_2026/7koo_22979_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7koo_22979/10_2026/7koo_22979_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 165 5.16 5 C 12210 2.51 5 N 3035 2.21 5 O 3500 1.98 5 H 18180 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37095 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6285 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1041 Classifications: {'peptide': 71} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 63} Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, G, H, I, J, M, O, Q, S, N, P, R, T Time building chain proxies: 8.55, per 1000 atoms: 0.23 Number of scatterers: 37095 At special positions: 0 Unit cell: (130.559, 129.48, 167.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 165 16.00 O 3500 8.00 N 3035 7.00 C 12210 6.00 H 18180 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 23 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 44 " distance=2.04 Simple disulfide: pdb=" SG CYS F 29 " - pdb=" SG CYS F 33 " distance=2.04 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 59 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 65 " distance=2.04 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 23 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 44 " distance=2.04 Simple disulfide: pdb=" SG CYS G 29 " - pdb=" SG CYS G 33 " distance=2.04 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 59 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 65 " distance=2.04 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 23 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 44 " distance=2.04 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 33 " distance=2.04 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 59 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 65 " distance=2.04 Simple disulfide: pdb=" SG CYS I 3 " - pdb=" SG CYS I 23 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 44 " distance=2.04 Simple disulfide: pdb=" SG CYS I 29 " - pdb=" SG CYS I 33 " distance=2.04 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 59 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 65 " distance=2.04 Simple disulfide: pdb=" SG CYS J 3 " - pdb=" SG CYS J 23 " distance=2.03 Simple disulfide: pdb=" SG CYS J 16 " - pdb=" SG CYS J 44 " distance=2.04 Simple disulfide: pdb=" SG CYS J 29 " - pdb=" SG CYS J 33 " distance=2.04 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 59 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 65 " 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 ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " BETA1-4 " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG B 501 " - " ASN B 67 " " NAG C 501 " - " ASN C 67 " " NAG D 501 " - " ASN D 67 " " NAG E 501 " - " ASN E 67 " " NAG K 1 " - " ASN A 110 " " NAG L 1 " - " ASN A 23 " " NAG M 1 " - " ASN B 110 " " NAG N 1 " - " ASN B 23 " " NAG O 1 " - " ASN C 110 " " NAG P 1 " - " ASN C 23 " " NAG Q 1 " - " ASN D 110 " " NAG R 1 " - " ASN D 23 " " NAG S 1 " - " ASN E 110 " " NAG T 1 " - " ASN E 23 " Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 38.3% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.569A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 321 removed outlier: 3.646A pdb=" N ARG A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 465 removed outlier: 3.516A pdb=" N GLU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.521A pdb=" N SER A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.513A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 84' Processing helix chain 'B' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.646A pdb=" N ARG B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 465 removed outlier: 3.517A pdb=" N GLU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 416 " --> pdb=" O LYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.520A pdb=" N SER B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.514A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.701A pdb=" N GLN C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'C' and resid 207 through 214 removed outlier: 4.066A pdb=" N LEU C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.931A pdb=" N LEU C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 321 removed outlier: 3.647A pdb=" N ARG C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 465 removed outlier: 3.517A pdb=" N GLU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C 416 " --> pdb=" O LYS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.520A pdb=" N SER C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.514A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D 84 " --> pdb=" O ASP D 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 84' Processing helix chain 'D' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 227 Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 321 removed outlier: 3.646A pdb=" N ARG D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 465 removed outlier: 3.516A pdb=" N GLU D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 416 " --> pdb=" O LYS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.521A pdb=" N SER D 475 " --> pdb=" O VAL D 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.514A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE E 84 " --> pdb=" O ASP E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 84' Processing helix chain 'E' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 227 Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU E 254 " --> pdb=" O THR E 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 321 removed outlier: 3.647A pdb=" N ARG E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 465 removed outlier: 3.517A pdb=" N GLU E 415 " --> pdb=" O ALA E 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU E 416 " --> pdb=" O LYS E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 478 removed outlier: 3.521A pdb=" N SER E 475 " --> pdb=" O VAL E 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN A 110 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN A 110 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY A 146 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY A 146 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 21.375A pdb=" N ARG A 182 " --> pdb=" O CYS F 44 " (cutoff:3.500A) removed outlier: 18.350A pdb=" N CYS F 44 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 12.130A pdb=" N GLU A 184 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU F 42 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE A 186 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 22 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN B 110 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN B 110 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.523A pdb=" N GLY B 146 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.523A pdb=" N GLY B 146 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 21.147A pdb=" N ARG B 182 " --> pdb=" O CYS G 44 " (cutoff:3.500A) removed outlier: 18.147A pdb=" N CYS G 44 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N GLU B 184 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N LEU G 42 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE B 186 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 22 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 29 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY C 146 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY C 146 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 21.090A pdb=" N ARG C 182 " --> pdb=" O CYS H 44 " (cutoff:3.500A) removed outlier: 18.140A pdb=" N CYS H 44 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 11.887A pdb=" N GLU C 184 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N LEU H 42 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE C 186 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU H 22 " --> pdb=" O ALA H 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN D 110 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN D 110 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR D 60 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR D 29 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY D 146 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY D 146 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 21.338A pdb=" N ARG D 182 " --> pdb=" O CYS I 44 " (cutoff:3.500A) removed outlier: 18.360A pdb=" N CYS I 44 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 12.052A pdb=" N GLU D 184 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LEU I 42 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE D 186 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU I 22 " --> pdb=" O ALA I 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN E 110 " --> pdb=" O HIS E 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN E 110 " --> pdb=" O HIS E 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR E 60 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR E 29 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.523A pdb=" N GLY E 146 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.523A pdb=" N GLY E 146 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 21.218A pdb=" N ARG E 182 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 18.273A pdb=" N CYS J 44 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N GLU E 184 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N LEU J 42 " --> pdb=" O GLU E 184 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE E 186 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU J 22 " --> pdb=" O ALA J 45 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2940 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: 10.89 Time building geometry restraints manager: 5.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18135 1.03 - 1.23: 336 1.23 - 1.43: 7859 1.43 - 1.62: 11045 1.62 - 1.82: 220 Bond restraints: 37595 Sorted by residual: bond pdb=" C ALA E 101 " pdb=" N THR E 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.37e+01 bond pdb=" C ALA B 101 " pdb=" N THR B 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.37e+01 bond pdb=" C ALA A 101 " pdb=" N THR A 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.35e+01 bond pdb=" C ALA D 101 " pdb=" N THR D 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.35e+01 bond pdb=" C ALA C 101 " pdb=" N THR C 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.33e+01 ... (remaining 37590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 67607 5.28 - 10.57: 183 10.57 - 15.85: 35 15.85 - 21.13: 5 21.13 - 26.41: 15 Bond angle restraints: 67845 Sorted by residual: angle pdb=" CB LEU D 292 " pdb=" CG LEU D 292 " pdb=" HG LEU D 292 " ideal model delta sigma weight residual 109.00 82.59 26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CB LEU B 292 " pdb=" CG LEU B 292 " pdb=" HG LEU B 292 " ideal model delta sigma weight residual 109.00 82.59 26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CB LEU A 292 " pdb=" CG LEU A 292 " pdb=" HG LEU A 292 " ideal model delta sigma weight residual 109.00 82.59 26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CB LEU E 292 " pdb=" CG LEU E 292 " pdb=" HG LEU E 292 " ideal model delta sigma weight residual 109.00 82.61 26.39 3.00e+00 1.11e-01 7.74e+01 angle pdb=" CB LEU C 292 " pdb=" CG LEU C 292 " pdb=" HG LEU C 292 " ideal model delta sigma weight residual 109.00 82.61 26.39 3.00e+00 1.11e-01 7.74e+01 ... (remaining 67840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 17199 22.10 - 44.19: 901 44.19 - 66.29: 215 66.29 - 88.39: 58 88.39 - 110.49: 32 Dihedral angle restraints: 18405 sinusoidal: 10160 harmonic: 8245 Sorted by residual: dihedral pdb=" CB CYS G 60 " pdb=" SG CYS G 60 " pdb=" SG CYS G 65 " pdb=" CB CYS G 65 " ideal model delta sinusoidal sigma weight residual -86.00 -37.56 -48.44 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS J 60 " pdb=" SG CYS J 60 " pdb=" SG CYS J 65 " pdb=" CB CYS J 65 " ideal model delta sinusoidal sigma weight residual -86.00 -37.58 -48.42 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS I 60 " pdb=" SG CYS I 60 " pdb=" SG CYS I 65 " pdb=" CB CYS I 65 " ideal model delta sinusoidal sigma weight residual -86.00 -37.60 -48.40 1 1.00e+01 1.00e-02 3.23e+01 ... (remaining 18402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 3080 0.347 - 0.694: 5 0.694 - 1.041: 0 1.041 - 1.388: 0 1.388 - 1.735: 5 Chirality restraints: 3090 Sorted by residual: chirality pdb=" CG LEU C 292 " pdb=" CB LEU C 292 " pdb=" CD1 LEU C 292 " pdb=" CD2 LEU C 292 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.53e+01 chirality pdb=" CG LEU E 292 " pdb=" CB LEU E 292 " pdb=" CD1 LEU E 292 " pdb=" CD2 LEU E 292 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.73 2.00e-01 2.50e+01 7.52e+01 chirality pdb=" CG LEU B 292 " pdb=" CB LEU B 292 " pdb=" CD1 LEU B 292 " pdb=" CD2 LEU B 292 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.73 2.00e-01 2.50e+01 7.52e+01 ... (remaining 3087 not shown) Planarity restraints: 5420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 469 " -0.075 2.00e-02 2.50e+03 7.63e-02 8.73e+01 pdb=" CG ASN C 469 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 469 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN C 469 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN C 469 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN C 469 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 469 " -0.075 2.00e-02 2.50e+03 7.61e-02 8.70e+01 pdb=" CG ASN B 469 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 469 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN B 469 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 469 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN B 469 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 469 " -0.075 2.00e-02 2.50e+03 7.61e-02 8.69e+01 pdb=" CG ASN E 469 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN E 469 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN E 469 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN E 469 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN E 469 " 0.107 2.00e-02 2.50e+03 ... (remaining 5417 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 598 2.08 - 2.71: 60129 2.71 - 3.34: 102023 3.34 - 3.97: 131964 3.97 - 4.60: 212097 Nonbonded interactions: 506811 Sorted by model distance: nonbonded pdb="HH22 ARG A 98 " pdb=" O GLU E 97 " model vdw 1.447 2.450 nonbonded pdb=" OD1 ASP D 88 " pdb=" HG SER D 147 " model vdw 1.543 2.450 nonbonded pdb=" OD1 ASP A 88 " pdb=" HG SER A 147 " model vdw 1.544 2.450 nonbonded pdb=" OD1 ASP B 88 " pdb=" HG SER B 147 " model vdw 1.544 2.450 nonbonded pdb=" OD1 ASP C 88 " pdb=" HG SER C 147 " model vdw 1.544 2.450 ... (remaining 506806 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.470 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 41.030 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:10.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.010 0.120 19480 Z= 0.510 Angle : 1.148 17.285 26615 Z= 0.678 Chirality : 0.090 1.735 3090 Planarity : 0.007 0.043 3250 Dihedral : 15.631 110.487 7545 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.20 % Allowed : 1.44 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2285 helix: 0.55 (0.17), residues: 905 sheet: -0.78 (0.22), residues: 475 loop : -1.17 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG I 25 TYR 0.039 0.003 TYR C 187 PHE 0.068 0.004 PHE C 452 TRP 0.016 0.002 TRP C 59 HIS 0.014 0.002 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00977 / 0.51 (19415) covalent geometry : angle 1.13539 / 0.68 (26450) SS BOND : bond 0.00409 / 0.24 ( 30) SS BOND : angle 1.81109 / 1.32 ( 60) hydrogen bonds : bond 0.13010 / 8.61 ( 910) hydrogen bonds : angle 6.39753 / 4.46 ( 2940) link_ALPHA1-3 : bond 0.00366 / 0.20 ( 5) link_ALPHA1-3 : angle 1.65730 / 0.95 ( 15) link_BETA1-4 : bond 0.01179 / 0.62 ( 15) link_BETA1-4 : angle 1.76512 / 1.11 ( 45) link_NAG-ASN : bond 0.00261 / 0.13 ( 15) link_NAG-ASN : angle 3.58812 / 2.33 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 1.016 Fit side-chains REVERT: A 93 ASN cc_start: 0.8732 (p0) cc_final: 0.8352 (p0) REVERT: A 227 LEU cc_start: 0.8357 (tp) cc_final: 0.7985 (tp) REVERT: B 43 ASP cc_start: 0.7726 (t0) cc_final: 0.7478 (t0) REVERT: B 465 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7178 (mmm) REVERT: C 193 PRO cc_start: 0.8900 (OUTLIER) cc_final: 0.8585 (Cg_endo) REVERT: D 193 PRO cc_start: 0.8868 (OUTLIER) cc_final: 0.8530 (Cg_endo) REVERT: E 52 ASN cc_start: 0.8347 (t0) cc_final: 0.8083 (t0) REVERT: E 193 PRO cc_start: 0.8723 (OUTLIER) cc_final: 0.8370 (Cg_endo) REVERT: F 58 THR cc_start: 0.7634 (m) cc_final: 0.7396 (m) outliers start: 25 outliers final: 9 residues processed: 291 average time/residue: 0.7433 time to fit residues: 265.7220 Evaluate side-chains 203 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 193 PRO Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 193 PRO Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 193 PRO Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain I residue 62 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN B 46 ASN C 38 GLN C 52 ASN D 38 GLN E 46 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.181509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126540 restraints weight = 57520.224| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.09 r_work: 0.3133 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19480 Z= 0.143 Angle : 0.656 11.538 26615 Z= 0.324 Chirality : 0.081 1.737 3090 Planarity : 0.006 0.048 3250 Dihedral : 10.280 72.144 3223 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.53 % Allowed : 8.63 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2285 helix: 1.33 (0.17), residues: 890 sheet: -0.74 (0.20), residues: 555 loop : -0.80 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 204 TYR 0.012 0.001 TYR B 419 PHE 0.014 0.001 PHE A 452 TRP 0.011 0.001 TRP E 59 HIS 0.002 0.001 HIS E 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (19415) covalent geometry : angle 0.63867 / 0.32 (26450) SS BOND : bond 0.00297 / 0.18 ( 30) SS BOND : angle 1.35770 / 1.01 ( 60) hydrogen bonds : bond 0.05254 / 3.39 ( 910) hydrogen bonds : angle 4.96806 / 3.46 ( 2940) link_ALPHA1-3 : bond 0.00905 / 0.49 ( 5) link_ALPHA1-3 : angle 1.72566 / 0.96 ( 15) link_BETA1-4 : bond 0.00456 / 0.28 ( 15) link_BETA1-4 : angle 1.76955 / 1.16 ( 45) link_NAG-ASN : bond 0.00303 / 0.18 ( 15) link_NAG-ASN : angle 2.85913 / 1.80 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8519 (tptt) cc_final: 0.8170 (tppt) REVERT: A 227 LEU cc_start: 0.8010 (tp) cc_final: 0.7768 (tp) REVERT: A 450 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5967 (mtt) REVERT: A 472 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5621 (mp0) REVERT: B 45 LYS cc_start: 0.8614 (tptt) cc_final: 0.8279 (tppt) REVERT: B 239 ILE cc_start: 0.6744 (mm) cc_final: 0.6450 (mm) REVERT: B 437 TRP cc_start: 0.5396 (m100) cc_final: 0.4795 (m-10) REVERT: C 43 ASP cc_start: 0.8007 (t0) cc_final: 0.7772 (t0) REVERT: C 45 LYS cc_start: 0.8568 (tptt) cc_final: 0.8063 (tppt) REVERT: C 116 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: C 437 TRP cc_start: 0.5305 (m100) cc_final: 0.4929 (m-10) REVERT: D 288 THR cc_start: 0.6830 (OUTLIER) cc_final: 0.6572 (t) REVERT: D 437 TRP cc_start: 0.5366 (m100) cc_final: 0.5070 (m-10) REVERT: E 52 ASN cc_start: 0.8866 (t0) cc_final: 0.8615 (t0) REVERT: J 20 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6478 (mt-10) outliers start: 32 outliers final: 9 residues processed: 221 average time/residue: 0.7768 time to fit residues: 209.0675 Evaluate side-chains 191 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [160, 119, 195, 120, 13, 89, 179, 2, 34, 220, 28] chunk 160 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN D 116 GLN E 38 GLN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109677 restraints weight = 57439.561| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.01 r_work: 0.3045 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19480 Z= 0.199 Angle : 0.655 11.309 26615 Z= 0.324 Chirality : 0.082 1.729 3090 Planarity : 0.005 0.045 3250 Dihedral : 8.127 57.776 3202 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.82 % Allowed : 9.59 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2285 helix: 1.46 (0.17), residues: 890 sheet: -0.44 (0.21), residues: 550 loop : -0.72 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 98 TYR 0.010 0.002 TYR E 194 PHE 0.014 0.001 PHE B 99 TRP 0.014 0.001 TRP E 437 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (19415) covalent geometry : angle 0.63761 / 0.32 (26450) SS BOND : bond 0.00855 / 0.53 ( 30) SS BOND : angle 1.53145 / 1.09 ( 60) hydrogen bonds : bond 0.05165 / 3.31 ( 910) hydrogen bonds : angle 4.84979 / 3.37 ( 2940) link_ALPHA1-3 : bond 0.01069 / 0.58 ( 5) link_ALPHA1-3 : angle 1.90363 / 1.05 ( 15) link_BETA1-4 : bond 0.00453 / 0.27 ( 15) link_BETA1-4 : angle 2.03367 / 1.35 ( 45) link_NAG-ASN : bond 0.00191 / 0.12 ( 15) link_NAG-ASN : angle 2.49637 / 1.55 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.982 Fit side-chains REVERT: A 45 LYS cc_start: 0.8527 (tptt) cc_final: 0.8154 (tppt) REVERT: A 472 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5600 (mp0) REVERT: B 45 LYS cc_start: 0.8713 (tptt) cc_final: 0.7976 (tppt) REVERT: B 437 TRP cc_start: 0.5681 (m100) cc_final: 0.5108 (m-10) REVERT: C 43 ASP cc_start: 0.8178 (t0) cc_final: 0.7906 (t0) REVERT: C 45 LYS cc_start: 0.8613 (tptt) cc_final: 0.8091 (tppt) REVERT: D 272 GLN cc_start: 0.7450 (mt0) cc_final: 0.7203 (mt0) REVERT: D 450 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.5840 (mtm) REVERT: E 116 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: E 304 MET cc_start: 0.4339 (ttm) cc_final: 0.4125 (ttm) REVERT: G 41 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8305 (mt-10) REVERT: I 3 CYS cc_start: 0.6768 (m) cc_final: 0.6367 (m) outliers start: 38 outliers final: 17 residues processed: 207 average time/residue: 0.8204 time to fit residues: 206.1358 Evaluate side-chains 195 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [133, 205, 1, 47, 30, 83, 123, 176, 38, 196, 180] chunk 133 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 0.0270 chunk 83 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 196 optimal weight: 0.0570 chunk 180 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 GLN ** E 295 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 = 0.3966 r_free = 0.3966 target = 0.175531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.116680 restraints weight = 56849.110| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.35 r_work: 0.3050 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19480 Z= 0.111 Angle : 0.577 11.310 26615 Z= 0.283 Chirality : 0.080 1.709 3090 Planarity : 0.005 0.046 3250 Dihedral : 6.809 58.332 3202 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.53 % Allowed : 10.50 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2285 helix: 1.83 (0.17), residues: 880 sheet: -0.20 (0.22), residues: 550 loop : -0.53 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 98 TYR 0.009 0.001 TYR E 273 PHE 0.009 0.001 PHE F 32 TRP 0.014 0.001 TRP E 437 HIS 0.003 0.000 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (19415) covalent geometry : angle 0.55876 / 0.28 (26450) SS BOND : bond 0.00296 / 0.17 ( 30) SS BOND : angle 1.66586 / 1.23 ( 60) hydrogen bonds : bond 0.04531 / 2.92 ( 910) hydrogen bonds : angle 4.53402 / 3.15 ( 2940) link_ALPHA1-3 : bond 0.01233 / 0.66 ( 5) link_ALPHA1-3 : angle 2.14671 / 1.20 ( 15) link_BETA1-4 : bond 0.00439 / 0.26 ( 15) link_BETA1-4 : angle 1.61937 / 1.08 ( 45) link_NAG-ASN : bond 0.00311 / 0.20 ( 15) link_NAG-ASN : angle 2.28454 / 1.43 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.988 Fit side-chains REVERT: A 45 LYS cc_start: 0.8559 (tptt) cc_final: 0.8270 (tppt) REVERT: A 472 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5619 (mp0) REVERT: B 45 LYS cc_start: 0.8465 (tptt) cc_final: 0.8109 (tppt) REVERT: B 437 TRP cc_start: 0.5668 (m100) cc_final: 0.5132 (m-10) REVERT: C 43 ASP cc_start: 0.8197 (t0) cc_final: 0.7882 (t0) REVERT: C 45 LYS cc_start: 0.8607 (tptt) cc_final: 0.8057 (tppt) REVERT: C 116 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: C 450 MET cc_start: 0.6324 (ttp) cc_final: 0.6062 (mtm) REVERT: D 272 GLN cc_start: 0.7383 (mt0) cc_final: 0.7096 (mt0) REVERT: D 450 MET cc_start: 0.6223 (OUTLIER) cc_final: 0.5904 (mtm) REVERT: E 116 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: G 41 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8295 (mt-10) outliers start: 32 outliers final: 12 residues processed: 202 average time/residue: 0.7860 time to fit residues: 192.6819 Evaluate side-chains 194 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [123, 171, 153, 33, 55, 176, 64, 37, 81, 38, 91] chunk 123 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN D 56 GLN E 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.170093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112546 restraints weight = 56900.164| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.92 r_work: 0.3000 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19480 Z= 0.215 Angle : 0.660 10.918 26615 Z= 0.327 Chirality : 0.082 1.721 3090 Planarity : 0.005 0.046 3250 Dihedral : 6.353 54.172 3202 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.35 % Allowed : 10.17 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.17), residues: 2285 helix: 1.70 (0.17), residues: 880 sheet: -0.25 (0.22), residues: 550 loop : -0.71 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 98 TYR 0.012 0.002 TYR B 194 PHE 0.014 0.002 PHE A 99 TRP 0.018 0.001 TRP E 437 HIS 0.004 0.001 HIS D 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.21 (19415) covalent geometry : angle 0.64158 / 0.32 (26450) SS BOND : bond 0.00667 / 0.32 ( 30) SS BOND : angle 1.89829 / 1.36 ( 60) hydrogen bonds : bond 0.04829 / 3.12 ( 910) hydrogen bonds : angle 4.68067 / 3.25 ( 2940) link_ALPHA1-3 : bond 0.01071 / 0.57 ( 5) link_ALPHA1-3 : angle 2.07872 / 1.16 ( 15) link_BETA1-4 : bond 0.00375 / 0.22 ( 15) link_BETA1-4 : angle 2.08391 / 1.38 ( 45) link_NAG-ASN : bond 0.00203 / 0.11 ( 15) link_NAG-ASN : angle 2.23921 / 1.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8550 (tptt) cc_final: 0.8278 (tppt) REVERT: A 253 MET cc_start: 0.6405 (mmp) cc_final: 0.6115 (mmp) REVERT: A 259 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6802 (tp) REVERT: B 45 LYS cc_start: 0.8627 (tptt) cc_final: 0.8261 (tppt) REVERT: B 272 GLN cc_start: 0.6912 (mt0) cc_final: 0.6487 (mt0) REVERT: B 437 TRP cc_start: 0.6071 (m100) cc_final: 0.5581 (m-10) REVERT: B 465 MET cc_start: 0.6961 (tpt) cc_final: 0.6143 (mmm) REVERT: C 45 LYS cc_start: 0.8643 (tptt) cc_final: 0.8338 (tppt) REVERT: C 116 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: C 161 GLU cc_start: 0.8433 (mp0) cc_final: 0.7993 (mp0) REVERT: C 450 MET cc_start: 0.6574 (ttp) cc_final: 0.6326 (mtm) REVERT: D 116 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: D 272 GLN cc_start: 0.7608 (mt0) cc_final: 0.7323 (mt0) REVERT: D 450 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6118 (mtm) REVERT: E 116 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: E 295 HIS cc_start: 0.4574 (t70) cc_final: 0.4218 (t-90) REVERT: E 304 MET cc_start: 0.4507 (ttm) cc_final: 0.4256 (ttm) REVERT: E 464 LEU cc_start: 0.7285 (mp) cc_final: 0.6974 (mm) REVERT: G 41 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8238 (mt-10) outliers start: 49 outliers final: 24 residues processed: 226 average time/residue: 0.7490 time to fit residues: 206.5938 Evaluate side-chains 222 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [208, 229, 63, 105, 135, 87, 122, 113, 101, 44, 10] chunk 208 optimal weight: 0.1980 chunk 229 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114375 restraints weight = 56966.748| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.97 r_work: 0.3042 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19480 Z= 0.117 Angle : 0.579 11.176 26615 Z= 0.286 Chirality : 0.080 1.708 3090 Planarity : 0.005 0.045 3250 Dihedral : 5.954 54.263 3202 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.63 % Allowed : 11.37 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2285 helix: 1.88 (0.17), residues: 880 sheet: -0.10 (0.22), residues: 550 loop : -0.55 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 25 TYR 0.010 0.001 TYR A 128 PHE 0.011 0.001 PHE C 99 TRP 0.015 0.001 TRP E 437 HIS 0.005 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (19415) covalent geometry : angle 0.56229 / 0.28 (26450) SS BOND : bond 0.00601 / 0.29 ( 30) SS BOND : angle 1.79177 / 1.38 ( 60) hydrogen bonds : bond 0.04391 / 2.83 ( 910) hydrogen bonds : angle 4.47684 / 3.11 ( 2940) link_ALPHA1-3 : bond 0.01133 / 0.61 ( 5) link_ALPHA1-3 : angle 1.91863 / 1.08 ( 15) link_BETA1-4 : bond 0.00402 / 0.24 ( 15) link_BETA1-4 : angle 1.55968 / 1.03 ( 45) link_NAG-ASN : bond 0.00233 / 0.15 ( 15) link_NAG-ASN : angle 2.06928 / 1.27 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8571 (tptt) cc_final: 0.8281 (tppt) REVERT: A 253 MET cc_start: 0.6352 (mmp) cc_final: 0.6099 (mmp) REVERT: A 472 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5823 (mp0) REVERT: B 45 LYS cc_start: 0.8641 (tptt) cc_final: 0.8261 (tppt) REVERT: B 437 TRP cc_start: 0.6106 (m100) cc_final: 0.5591 (m-10) REVERT: B 465 MET cc_start: 0.6944 (tpt) cc_final: 0.6121 (mmm) REVERT: C 45 LYS cc_start: 0.8606 (tptt) cc_final: 0.8287 (tppt) REVERT: C 116 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: C 450 MET cc_start: 0.6561 (ttp) cc_final: 0.6311 (mtm) REVERT: D 450 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6121 (mtm) REVERT: E 295 HIS cc_start: 0.4590 (t70) cc_final: 0.4342 (t-90) REVERT: E 472 GLU cc_start: 0.5506 (mp0) cc_final: 0.5266 (mp0) REVERT: G 41 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8357 (mt-10) REVERT: I 3 CYS cc_start: 0.6985 (m) cc_final: 0.6447 (m) outliers start: 34 outliers final: 21 residues processed: 216 average time/residue: 0.7548 time to fit residues: 199.5723 Evaluate side-chains 210 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain E residue 450 MET Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [177, 152, 81, 188, 56, 127, 168, 216, 126, 190, 134] chunk 177 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 216 optimal weight: 0.1980 chunk 126 optimal weight: 0.4980 chunk 190 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 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 = 0.3976 r_free = 0.3976 target = 0.175232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.117944 restraints weight = 57892.412| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.13 r_work: 0.3150 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19480 Z= 0.107 Angle : 0.554 11.154 26615 Z= 0.272 Chirality : 0.079 1.707 3090 Planarity : 0.004 0.044 3250 Dihedral : 5.577 54.981 3202 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 11.85 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.18), residues: 2285 helix: 2.02 (0.17), residues: 880 sheet: -0.05 (0.22), residues: 550 loop : -0.47 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.010 0.001 TYR A 128 PHE 0.010 0.001 PHE C 274 TRP 0.018 0.001 TRP D 437 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (19415) covalent geometry : angle 0.53930 / 0.27 (26450) SS BOND : bond 0.00311 / 0.19 ( 30) SS BOND : angle 1.60402 / 1.25 ( 60) hydrogen bonds : bond 0.04094 / 2.65 ( 910) hydrogen bonds : angle 4.30912 / 3.00 ( 2940) link_ALPHA1-3 : bond 0.00931 / 0.50 ( 5) link_ALPHA1-3 : angle 1.69450 / 0.96 ( 15) link_BETA1-4 : bond 0.00380 / 0.23 ( 15) link_BETA1-4 : angle 1.51880 / 1.01 ( 45) link_NAG-ASN : bond 0.00212 / 0.14 ( 15) link_NAG-ASN : angle 1.95442 / 1.20 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.6511 (mmp) cc_final: 0.6144 (mmp) REVERT: A 472 GLU cc_start: 0.6207 (mt-10) cc_final: 0.5990 (mp0) REVERT: B 437 TRP cc_start: 0.6069 (m100) cc_final: 0.5533 (m-10) REVERT: B 444 VAL cc_start: 0.7025 (p) cc_final: 0.6794 (p) REVERT: B 465 MET cc_start: 0.7052 (tpt) cc_final: 0.6247 (mmm) REVERT: C 45 LYS cc_start: 0.8590 (tptt) cc_final: 0.8322 (tppt) REVERT: C 116 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: C 450 MET cc_start: 0.6627 (ttp) cc_final: 0.6411 (mtm) REVERT: D 450 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6449 (mtm) REVERT: I 3 CYS cc_start: 0.6999 (m) cc_final: 0.6571 (m) outliers start: 29 outliers final: 14 residues processed: 214 average time/residue: 0.7479 time to fit residues: 196.5910 Evaluate side-chains 201 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [204, 166, 129, 161, 54, 27, 197, 183, 122, 26, 108] chunk 204 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 0.0040 chunk 108 optimal weight: 7.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.174305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117404 restraints weight = 57667.267| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.69 r_work: 0.2998 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19480 Z= 0.124 Angle : 0.566 11.123 26615 Z= 0.278 Chirality : 0.079 1.707 3090 Planarity : 0.004 0.045 3250 Dihedral : 5.498 54.538 3202 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.53 % Allowed : 12.04 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2285 helix: 2.04 (0.17), residues: 880 sheet: -0.05 (0.22), residues: 550 loop : -0.47 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.010 0.001 TYR A 128 PHE 0.010 0.001 PHE A 99 TRP 0.021 0.001 TRP D 437 HIS 0.005 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (19415) covalent geometry : angle 0.55062 / 0.27 (26450) SS BOND : bond 0.00389 / 0.24 ( 30) SS BOND : angle 1.82849 / 1.37 ( 60) hydrogen bonds : bond 0.04077 / 2.64 ( 910) hydrogen bonds : angle 4.31304 / 3.01 ( 2940) link_ALPHA1-3 : bond 0.00861 / 0.46 ( 5) link_ALPHA1-3 : angle 1.65472 / 0.94 ( 15) link_BETA1-4 : bond 0.00376 / 0.23 ( 15) link_BETA1-4 : angle 1.54382 / 1.02 ( 45) link_NAG-ASN : bond 0.00180 / 0.12 ( 15) link_NAG-ASN : angle 1.91275 / 1.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.6317 (mmp) cc_final: 0.5914 (mmp) REVERT: A 259 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6438 (tp) REVERT: A 472 GLU cc_start: 0.6147 (mt-10) cc_final: 0.5927 (mp0) REVERT: B 272 GLN cc_start: 0.6938 (mt0) cc_final: 0.6567 (mt0) REVERT: B 437 TRP cc_start: 0.6045 (m100) cc_final: 0.5374 (m-10) REVERT: B 444 VAL cc_start: 0.6757 (p) cc_final: 0.6538 (p) REVERT: C 45 LYS cc_start: 0.8601 (tptt) cc_final: 0.8308 (tppt) REVERT: C 116 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: C 448 CYS cc_start: 0.6118 (t) cc_final: 0.5835 (p) REVERT: C 450 MET cc_start: 0.6465 (ttp) cc_final: 0.6244 (mtm) REVERT: D 450 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6342 (mtm) REVERT: E 161 GLU cc_start: 0.8240 (mp0) cc_final: 0.7875 (mp0) REVERT: I 3 CYS cc_start: 0.6920 (m) cc_final: 0.6482 (m) outliers start: 32 outliers final: 21 residues processed: 211 average time/residue: 0.7395 time to fit residues: 192.4435 Evaluate side-chains 209 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [104, 135, 115, 48, 63, 33, 163, 168, 116, 7, 186] chunk 104 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 186 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 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 = 0.3966 r_free = 0.3966 target = 0.174207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114011 restraints weight = 58109.457| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.97 r_work: 0.3085 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19480 Z= 0.120 Angle : 0.561 11.133 26615 Z= 0.275 Chirality : 0.079 1.704 3090 Planarity : 0.004 0.042 3250 Dihedral : 5.435 54.073 3202 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.49 % Allowed : 12.61 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2285 helix: 2.05 (0.17), residues: 880 sheet: -0.03 (0.22), residues: 550 loop : -0.44 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.009 0.001 TYR A 128 PHE 0.010 0.001 PHE A 99 TRP 0.026 0.001 TRP D 437 HIS 0.009 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (19415) covalent geometry : angle 0.54611 / 0.27 (26450) SS BOND : bond 0.00346 / 0.22 ( 30) SS BOND : angle 1.75602 / 1.30 ( 60) hydrogen bonds : bond 0.04016 / 2.61 ( 910) hydrogen bonds : angle 4.27045 / 2.97 ( 2940) link_ALPHA1-3 : bond 0.00791 / 0.42 ( 5) link_ALPHA1-3 : angle 1.57600 / 0.90 ( 15) link_BETA1-4 : bond 0.00402 / 0.24 ( 15) link_BETA1-4 : angle 1.47952 / 0.97 ( 45) link_NAG-ASN : bond 0.00182 / 0.12 ( 15) link_NAG-ASN : angle 1.86252 / 1.13 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.6692 (mmp) cc_final: 0.6279 (mmp) REVERT: A 259 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6466 (tp) REVERT: A 472 GLU cc_start: 0.6306 (mt-10) cc_final: 0.6088 (mp0) REVERT: B 272 GLN cc_start: 0.7155 (mt0) cc_final: 0.6785 (mt0) REVERT: B 437 TRP cc_start: 0.6223 (m100) cc_final: 0.5562 (m-10) REVERT: B 444 VAL cc_start: 0.7106 (OUTLIER) cc_final: 0.6863 (p) REVERT: C 116 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: C 128 TYR cc_start: 0.7463 (t80) cc_final: 0.6675 (t80) REVERT: C 450 MET cc_start: 0.6606 (ttp) cc_final: 0.6395 (mtm) REVERT: D 450 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6532 (mtm) REVERT: E 161 GLU cc_start: 0.8320 (mp0) cc_final: 0.7902 (mp0) REVERT: E 444 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7116 (p) REVERT: I 3 CYS cc_start: 0.7100 (m) cc_final: 0.6698 (m) outliers start: 31 outliers final: 20 residues processed: 210 average time/residue: 0.7527 time to fit residues: 194.9451 Evaluate side-chains 213 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [75, 138, 141, 154, 80, 115, 108, 5, 193, 209, 219] chunk 75 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.173076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114992 restraints weight = 57915.950| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.04 r_work: 0.3033 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19480 Z= 0.155 Angle : 0.591 11.069 26615 Z= 0.292 Chirality : 0.080 1.703 3090 Planarity : 0.005 0.045 3250 Dihedral : 5.576 52.781 3202 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.49 % Allowed : 12.61 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.17), residues: 2285 helix: 1.96 (0.17), residues: 880 sheet: -0.04 (0.22), residues: 550 loop : -0.54 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.009 0.001 TYR A 128 PHE 0.014 0.001 PHE A 99 TRP 0.033 0.001 TRP D 437 HIS 0.005 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 (19415) covalent geometry : angle 0.57606 / 0.29 (26450) SS BOND : bond 0.00419 / 0.27 ( 30) SS BOND : angle 1.91674 / 1.42 ( 60) hydrogen bonds : bond 0.04184 / 2.72 ( 910) hydrogen bonds : angle 4.36058 / 3.04 ( 2940) link_ALPHA1-3 : bond 0.00694 / 0.38 ( 5) link_ALPHA1-3 : angle 1.61766 / 0.91 ( 15) link_BETA1-4 : bond 0.00399 / 0.24 ( 15) link_BETA1-4 : angle 1.58810 / 1.03 ( 45) link_NAG-ASN : bond 0.00149 / 0.10 ( 15) link_NAG-ASN : angle 1.87773 / 1.13 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: A 259 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6472 (tp) REVERT: A 286 VAL cc_start: 0.7255 (t) cc_final: 0.6976 (m) REVERT: A 472 GLU cc_start: 0.6265 (mt-10) cc_final: 0.6052 (mp0) REVERT: B 272 GLN cc_start: 0.7200 (mt0) cc_final: 0.6575 (mt0) REVERT: B 437 TRP cc_start: 0.6332 (m100) cc_final: 0.5655 (m-10) REVERT: B 444 VAL cc_start: 0.7097 (OUTLIER) cc_final: 0.6854 (p) REVERT: C 116 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: C 128 TYR cc_start: 0.7479 (t80) cc_final: 0.6676 (t80) REVERT: C 450 MET cc_start: 0.6511 (ttp) cc_final: 0.6246 (mtm) REVERT: D 296 HIS cc_start: 0.5685 (m-70) cc_final: 0.5482 (m170) REVERT: D 450 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6549 (mtm) REVERT: E 161 GLU cc_start: 0.8346 (mp0) cc_final: 0.7925 (mp0) REVERT: E 444 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7129 (p) REVERT: I 3 CYS cc_start: 0.7074 (m) cc_final: 0.6674 (m) outliers start: 31 outliers final: 20 residues processed: 223 average time/residue: 0.7238 time to fit residues: 199.6297 Evaluate side-chains 222 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [76, 196, 28, 157, 41, 98, 105, 63, 48, 50, 60] chunk 76 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 157 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN E 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.174396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117887 restraints weight = 57392.591| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.65 r_work: 0.2975 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19480 Z= 0.142 Angle : 0.579 11.145 26615 Z= 0.285 Chirality : 0.079 1.700 3090 Planarity : 0.004 0.042 3250 Dihedral : 5.542 52.022 3202 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.44 % Allowed : 13.00 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2285 helix: 2.21 (0.17), residues: 850 sheet: -0.04 (0.22), residues: 550 loop : -0.64 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.010 0.001 TYR A 128 PHE 0.012 0.001 PHE A 99 TRP 0.034 0.001 TRP D 437 HIS 0.007 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (19415) covalent geometry : angle 0.56467 / 0.28 (26450) SS BOND : bond 0.00402 / 0.26 ( 30) SS BOND : angle 1.83867 / 1.36 ( 60) hydrogen bonds : bond 0.04127 / 2.69 ( 910) hydrogen bonds : angle 4.33479 / 3.02 ( 2940) link_ALPHA1-3 : bond 0.00696 / 0.37 ( 5) link_ALPHA1-3 : angle 1.57371 / 0.88 ( 15) link_BETA1-4 : bond 0.00434 / 0.26 ( 15) link_BETA1-4 : angle 1.45464 / 0.94 ( 45) link_NAG-ASN : bond 0.00168 / 0.11 ( 15) link_NAG-ASN : angle 1.86585 / 1.13 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10940.11 seconds wall clock time: 185 minutes 35.98 seconds (11135.98 seconds total)