Starting phenix.real_space_refine on Mon Jun 9 20:28:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mnh_48423/06_2025/9mnh_48423.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mnh_48423/06_2025/9mnh_48423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mnh_48423/06_2025/9mnh_48423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mnh_48423/06_2025/9mnh_48423.map" model { file = "/net/cci-nas-00/data/ceres_data/9mnh_48423/06_2025/9mnh_48423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mnh_48423/06_2025/9mnh_48423.cif" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6864 2.51 5 N 1758 2.21 5 O 2193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10875 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3495 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 21, 'TRANS': 439} Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3495 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 21, 'TRANS': 439} Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3495 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 21, 'TRANS': 439} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.18, per 1000 atoms: 0.66 Number of scatterers: 10875 At special positions: 0 Unit cell: (112.2, 112.2, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2193 8.00 N 1758 7.00 C 6864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 334 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 357 " distance=2.02 Simple disulfide: pdb=" SG CYS A 381 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 411 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 334 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 411 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 334 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 381 " - pdb=" SG CYS C 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 411 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " BETA1-6 " NAG E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG G 1 " - " FUC G 4 " " NAG I 1 " - " FUC I 4 " NAG-ASN " NAG A 601 " - " ASN A 434 " " NAG A 602 " - " ASN A 353 " " NAG A 603 " - " ASN A 458 " " NAG B 601 " - " ASN B 434 " " NAG B 602 " - " ASN B 353 " " NAG B 603 " - " ASN B 458 " " NAG C 601 " - " ASN C 434 " " NAG C 602 " - " ASN C 353 " " NAG C 603 " - " ASN C 458 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 93 " " NAG F 1 " - " ASN B 61 " " NAG G 1 " - " ASN B 93 " " NAG H 1 " - " ASN C 61 " " NAG I 1 " - " ASN C 93 " Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2574 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 21 sheets defined 37.8% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.569A pdb=" N LEU A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.729A pdb=" N THR A 63 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 64 " --> pdb=" O ASN A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 60 through 64' Processing helix chain 'A' and resid 69 through 95 removed outlier: 4.078A pdb=" N TYR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix removed outlier: 3.771A pdb=" N VAL A 95 " --> pdb=" O MET A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 118 through 140 removed outlier: 3.523A pdb=" N VAL A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN A 133 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASN A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.742A pdb=" N ASN A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 208 removed outlier: 3.623A pdb=" N THR A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.508A pdb=" N LEU A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.842A pdb=" N LEU A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.128A pdb=" N LEU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 446 through 478 Processing helix chain 'B' and resid 23 through 31 removed outlier: 3.540A pdb=" N LEU B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.792A pdb=" N THR B 63 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 64 " --> pdb=" O ASN B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 60 through 64' Processing helix chain 'B' and resid 69 through 94 removed outlier: 4.094A pdb=" N TYR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Proline residue: B 83 - end of helix removed outlier: 3.570A pdb=" N SER B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 140 removed outlier: 5.303A pdb=" N GLN B 133 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 185 through 208 removed outlier: 3.562A pdb=" N THR B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 213 removed outlier: 3.598A pdb=" N ARG B 213 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.857A pdb=" N LEU B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.315A pdb=" N LEU B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 446 through 479 removed outlier: 3.977A pdb=" N THR B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 476 " --> pdb=" O ASN B 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 31 removed outlier: 3.713A pdb=" N LEU C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.670A pdb=" N THR C 63 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 60 through 64' Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.067A pdb=" N TYR C 73 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA C 79 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Proline residue: C 83 - end of helix removed outlier: 3.656A pdb=" N SER C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.555A pdb=" N GLY C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 115' Processing helix chain 'C' and resid 118 through 140 removed outlier: 5.239A pdb=" N GLN C 133 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 171 through 176 removed outlier: 3.620A pdb=" N ASN C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 208 removed outlier: 3.544A pdb=" N THR C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 207 " --> pdb=" O GLN C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.969A pdb=" N LEU C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 252 removed outlier: 4.493A pdb=" N LEU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 247 through 252' Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 357 Processing helix chain 'C' and resid 448 through 479 removed outlier: 3.545A pdb=" N ASN C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 476 " --> pdb=" O ASN C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing sheet with id=AA1, first strand: chain 'A' and resid 279 through 281 Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281 removed outlier: 5.612A pdb=" N LYS A 34 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE A 291 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N HIS A 36 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 311 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 54 removed outlier: 3.766A pdb=" N THR A 47 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 271 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA5, first strand: chain 'A' and resid 155 through 156 Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 297 removed outlier: 4.010A pdb=" N LEU A 301 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AA8, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.927A pdb=" N LYS A 393 " --> pdb=" O CYS A 388 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET A 420 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 279 through 281 removed outlier: 5.595A pdb=" N LYS B 34 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE B 291 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS B 36 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 311 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 279 through 281 Processing sheet with id=AB2, first strand: chain 'B' and resid 47 through 54 removed outlier: 3.662A pdb=" N THR B 47 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 271 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR B 257 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 95 through 96 removed outlier: 6.780A pdb=" N VAL B 109 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS C 388 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS C 393 " --> pdb=" O CYS C 388 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AB5, first strand: chain 'B' and resid 155 through 156 Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 297 removed outlier: 4.009A pdb=" N LEU B 301 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 393 through 394 removed outlier: 3.958A pdb=" N LYS B 393 " --> pdb=" O CYS B 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 279 through 281 removed outlier: 5.533A pdb=" N LYS C 34 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE C 291 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N HIS C 36 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 311 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AC1, first strand: chain 'C' and resid 47 through 54 removed outlier: 3.767A pdb=" N THR C 47 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE C 271 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N THR C 257 " --> pdb=" O ASN C 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 155 through 156 Processing sheet with id=AC3, first strand: chain 'C' and resid 295 through 297 removed outlier: 3.980A pdb=" N LEU C 301 " --> pdb=" O VAL C 362 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3298 1.34 - 1.46: 1999 1.46 - 1.58: 5641 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11028 Sorted by residual: bond pdb=" N VAL C 95 " pdb=" CA VAL C 95 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.27e-02 6.20e+03 1.05e+01 bond pdb=" N LYS A 463 " pdb=" CA LYS A 463 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 9.97e+00 bond pdb=" N ILE C 104 " pdb=" CA ILE C 104 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.33e+00 bond pdb=" C SER C 462 " pdb=" N LYS C 463 " ideal model delta sigma weight residual 1.335 1.376 -0.040 1.38e-02 5.25e+03 8.61e+00 bond pdb=" N ILE C 108 " pdb=" CA ILE C 108 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.50e+00 ... (remaining 11023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 14601 2.79 - 5.57: 345 5.57 - 8.36: 65 8.36 - 11.14: 8 11.14 - 13.93: 2 Bond angle restraints: 15021 Sorted by residual: angle pdb=" C ASN A 101 " pdb=" CA ASN A 101 " pdb=" CB ASN A 101 " ideal model delta sigma weight residual 116.54 110.37 6.17 1.15e+00 7.56e-01 2.88e+01 angle pdb=" C ALA A 107 " pdb=" CA ALA A 107 " pdb=" CB ALA A 107 " ideal model delta sigma weight residual 116.63 111.21 5.42 1.16e+00 7.43e-01 2.18e+01 angle pdb=" CG1 ILE B 173 " pdb=" CB ILE B 173 " pdb=" CG2 ILE B 173 " ideal model delta sigma weight residual 110.70 96.77 13.93 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C LEU A 177 " pdb=" N VAL A 178 " pdb=" CA VAL A 178 " ideal model delta sigma weight residual 120.33 123.98 -3.65 8.00e-01 1.56e+00 2.08e+01 angle pdb=" C PRO B 100 " pdb=" N ASN B 101 " pdb=" CA ASN B 101 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 ... (remaining 15016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 6309 15.25 - 30.50: 644 30.50 - 45.75: 130 45.75 - 61.00: 49 61.00 - 76.25: 23 Dihedral angle restraints: 7155 sinusoidal: 3159 harmonic: 3996 Sorted by residual: dihedral pdb=" CA ASN B 456 " pdb=" C ASN B 456 " pdb=" N ILE B 457 " pdb=" CA ILE B 457 " ideal model delta harmonic sigma weight residual 180.00 151.02 28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLN C 419 " pdb=" C GLN C 419 " pdb=" N MET C 420 " pdb=" CA MET C 420 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CB CYS C 65 " pdb=" SG CYS C 65 " pdb=" SG CYS C 186 " pdb=" CB CYS C 186 " ideal model delta sinusoidal sigma weight residual 93.00 48.10 44.90 1 1.00e+01 1.00e-02 2.80e+01 ... (remaining 7152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1725 0.093 - 0.185: 209 0.185 - 0.278: 16 0.278 - 0.370: 2 0.370 - 0.463: 1 Chirality restraints: 1953 Sorted by residual: chirality pdb=" CB ILE B 104 " pdb=" CA ILE B 104 " pdb=" CG1 ILE B 104 " pdb=" CG2 ILE B 104 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CB ILE B 173 " pdb=" CA ILE B 173 " pdb=" CG1 ILE B 173 " pdb=" CG2 ILE B 173 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C2 NAG G 1 " pdb=" C1 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" N2 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.18 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1950 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 462 " -0.039 2.00e-02 2.50e+03 7.51e-02 5.64e+01 pdb=" C SER C 462 " 0.130 2.00e-02 2.50e+03 pdb=" O SER C 462 " -0.049 2.00e-02 2.50e+03 pdb=" N LYS C 463 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 462 " 0.033 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C SER A 462 " -0.112 2.00e-02 2.50e+03 pdb=" O SER A 462 " 0.042 2.00e-02 2.50e+03 pdb=" N LYS A 463 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 462 " 0.032 2.00e-02 2.50e+03 6.21e-02 3.85e+01 pdb=" C SER B 462 " -0.107 2.00e-02 2.50e+03 pdb=" O SER B 462 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS B 463 " 0.036 2.00e-02 2.50e+03 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2375 2.79 - 3.32: 9700 3.32 - 3.85: 17667 3.85 - 4.37: 18854 4.37 - 4.90: 32560 Nonbonded interactions: 81156 Sorted by model distance: nonbonded pdb=" O ASP C 476 " pdb=" OG1 THR C 479 " model vdw 2.267 3.040 nonbonded pdb=" OE1 GLN C 397 " pdb=" OG1 THR C 404 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLN B 397 " pdb=" OG1 THR B 404 " model vdw 2.288 3.040 nonbonded pdb=" OE1 GLN A 397 " pdb=" OG1 THR A 404 " model vdw 2.293 3.040 nonbonded pdb=" O ASN A 456 " pdb=" OG1 THR A 460 " model vdw 2.300 3.040 ... (remaining 81151 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.390 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11073 Z= 0.245 Angle : 1.077 20.152 15141 Z= 0.522 Chirality : 0.059 0.463 1953 Planarity : 0.007 0.075 1863 Dihedral : 13.650 76.245 4536 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.48 % Favored : 92.37 % Rotamer: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.19), residues: 1377 helix: -1.59 (0.20), residues: 455 sheet: -0.41 (0.31), residues: 240 loop : -2.03 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 302 HIS 0.002 0.001 HIS C 129 PHE 0.011 0.001 PHE C 229 TYR 0.019 0.002 TYR C 426 ARG 0.002 0.001 ARG A 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 15) link_NAG-ASN : angle 5.88778 ( 45) link_BETA1-4 : bond 0.01129 ( 12) link_BETA1-4 : angle 3.88955 ( 36) hydrogen bonds : bond 0.18614 ( 463) hydrogen bonds : angle 6.88370 ( 1302) link_BETA1-6 : bond 0.00469 ( 3) link_BETA1-6 : angle 1.48330 ( 9) SS BOND : bond 0.00278 ( 15) SS BOND : angle 0.92639 ( 30) covalent geometry : bond 0.00451 (11028) covalent geometry : angle 1.01280 (15021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.2096 time to fit residues: 16.6993 Evaluate side-chains 45 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.4980 chunk 104 optimal weight: 0.0670 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN B 139 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.058388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.046618 restraints weight = 51030.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046141 restraints weight = 56612.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046389 restraints weight = 63494.346| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11073 Z= 0.119 Angle : 0.651 14.580 15141 Z= 0.306 Chirality : 0.046 0.208 1953 Planarity : 0.004 0.042 1863 Dihedral : 7.235 59.308 2055 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1377 helix: -0.34 (0.23), residues: 467 sheet: -0.21 (0.33), residues: 217 loop : -1.80 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 302 HIS 0.001 0.000 HIS C 36 PHE 0.006 0.001 PHE C 208 TYR 0.009 0.001 TYR A 366 ARG 0.003 0.000 ARG A 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 15) link_NAG-ASN : angle 3.85664 ( 45) link_BETA1-4 : bond 0.00792 ( 12) link_BETA1-4 : angle 2.89442 ( 36) hydrogen bonds : bond 0.04831 ( 463) hydrogen bonds : angle 5.32789 ( 1302) link_BETA1-6 : bond 0.00377 ( 3) link_BETA1-6 : angle 1.31181 ( 9) SS BOND : bond 0.00192 ( 15) SS BOND : angle 0.54845 ( 30) covalent geometry : bond 0.00242 (11028) covalent geometry : angle 0.60043 (15021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 0.2064 time to fit residues: 17.3775 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 0.0670 chunk 93 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 101 optimal weight: 0.0970 chunk 88 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.0336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.043816 restraints weight = 51413.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.044249 restraints weight = 40952.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044404 restraints weight = 35402.670| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11073 Z= 0.129 Angle : 0.652 18.747 15141 Z= 0.301 Chirality : 0.046 0.354 1953 Planarity : 0.003 0.037 1863 Dihedral : 6.898 58.936 2055 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.21), residues: 1377 helix: 0.30 (0.24), residues: 464 sheet: -0.07 (0.33), residues: 215 loop : -1.67 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 302 HIS 0.003 0.001 HIS C 129 PHE 0.005 0.001 PHE B 105 TYR 0.010 0.001 TYR B 366 ARG 0.003 0.000 ARG C 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 15) link_NAG-ASN : angle 4.44918 ( 45) link_BETA1-4 : bond 0.00696 ( 12) link_BETA1-4 : angle 2.65693 ( 36) hydrogen bonds : bond 0.04331 ( 463) hydrogen bonds : angle 5.10653 ( 1302) link_BETA1-6 : bond 0.00359 ( 3) link_BETA1-6 : angle 1.26534 ( 9) SS BOND : bond 0.00230 ( 15) SS BOND : angle 0.39007 ( 30) covalent geometry : bond 0.00286 (11028) covalent geometry : angle 0.59253 (15021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 MET cc_start: 0.8113 (ttp) cc_final: 0.7910 (tmm) REVERT: B 420 MET cc_start: 0.8241 (mmp) cc_final: 0.8030 (mmp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2292 time to fit residues: 17.7691 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 453 GLN B 452 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.056308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.044637 restraints weight = 50378.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.044162 restraints weight = 60865.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044506 restraints weight = 65062.246| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11073 Z= 0.161 Angle : 0.669 13.094 15141 Z= 0.312 Chirality : 0.047 0.298 1953 Planarity : 0.003 0.039 1863 Dihedral : 6.928 59.619 2055 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.59 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1377 helix: 0.57 (0.24), residues: 463 sheet: -0.59 (0.31), residues: 241 loop : -1.59 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 302 HIS 0.005 0.001 HIS C 129 PHE 0.008 0.001 PHE A 229 TYR 0.011 0.001 TYR A 269 ARG 0.003 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 15) link_NAG-ASN : angle 3.58205 ( 45) link_BETA1-4 : bond 0.00667 ( 12) link_BETA1-4 : angle 2.54409 ( 36) hydrogen bonds : bond 0.04254 ( 463) hydrogen bonds : angle 5.15349 ( 1302) link_BETA1-6 : bond 0.00400 ( 3) link_BETA1-6 : angle 1.26581 ( 9) SS BOND : bond 0.00446 ( 15) SS BOND : angle 0.55749 ( 30) covalent geometry : bond 0.00365 (11028) covalent geometry : angle 0.62859 (15021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2082 time to fit residues: 16.2151 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 128 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 27 optimal weight: 0.0370 chunk 36 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.056817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.044317 restraints weight = 51365.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044333 restraints weight = 50952.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.044578 restraints weight = 49728.162| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11073 Z= 0.118 Angle : 0.643 17.980 15141 Z= 0.294 Chirality : 0.047 0.407 1953 Planarity : 0.003 0.036 1863 Dihedral : 6.725 59.791 2055 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1377 helix: 0.82 (0.24), residues: 464 sheet: -0.64 (0.31), residues: 241 loop : -1.48 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 302 HIS 0.002 0.001 HIS C 129 PHE 0.005 0.001 PHE B 229 TYR 0.010 0.001 TYR C 426 ARG 0.001 0.000 ARG A 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 15) link_NAG-ASN : angle 4.27131 ( 45) link_BETA1-4 : bond 0.00648 ( 12) link_BETA1-4 : angle 2.47568 ( 36) hydrogen bonds : bond 0.03828 ( 463) hydrogen bonds : angle 4.97023 ( 1302) link_BETA1-6 : bond 0.00336 ( 3) link_BETA1-6 : angle 1.21748 ( 9) SS BOND : bond 0.00200 ( 15) SS BOND : angle 0.55400 ( 30) covalent geometry : bond 0.00261 (11028) covalent geometry : angle 0.58828 (15021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.222 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1959 time to fit residues: 15.1107 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 453 GLN ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.044205 restraints weight = 51251.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.044082 restraints weight = 54865.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.044385 restraints weight = 54387.151| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11073 Z= 0.140 Angle : 0.659 15.175 15141 Z= 0.304 Chirality : 0.047 0.456 1953 Planarity : 0.003 0.035 1863 Dihedral : 6.721 58.990 2055 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.88 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1377 helix: 0.83 (0.24), residues: 470 sheet: -0.57 (0.31), residues: 239 loop : -1.48 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 302 HIS 0.004 0.001 HIS C 129 PHE 0.004 0.001 PHE A 290 TYR 0.017 0.001 TYR B 40 ARG 0.002 0.000 ARG C 359 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 15) link_NAG-ASN : angle 3.87844 ( 45) link_BETA1-4 : bond 0.00659 ( 12) link_BETA1-4 : angle 2.43145 ( 36) hydrogen bonds : bond 0.03777 ( 463) hydrogen bonds : angle 4.97091 ( 1302) link_BETA1-6 : bond 0.00373 ( 3) link_BETA1-6 : angle 1.37287 ( 9) SS BOND : bond 0.00227 ( 15) SS BOND : angle 0.66379 ( 30) covalent geometry : bond 0.00319 (11028) covalent geometry : angle 0.61385 (15021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.199 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1926 time to fit residues: 14.9491 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.0010 chunk 105 optimal weight: 0.0470 chunk 57 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 453 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.057285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.044788 restraints weight = 51771.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.044684 restraints weight = 51149.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.044975 restraints weight = 52276.650| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11073 Z= 0.103 Angle : 0.624 13.737 15141 Z= 0.287 Chirality : 0.046 0.356 1953 Planarity : 0.003 0.033 1863 Dihedral : 6.707 59.225 2055 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.59 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1377 helix: 1.06 (0.25), residues: 470 sheet: -0.57 (0.31), residues: 239 loop : -1.42 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 302 HIS 0.002 0.000 HIS C 129 PHE 0.007 0.001 PHE A 350 TYR 0.011 0.001 TYR C 426 ARG 0.001 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 15) link_NAG-ASN : angle 3.60784 ( 45) link_BETA1-4 : bond 0.00645 ( 12) link_BETA1-4 : angle 2.37757 ( 36) hydrogen bonds : bond 0.03384 ( 463) hydrogen bonds : angle 4.75995 ( 1302) link_BETA1-6 : bond 0.00332 ( 3) link_BETA1-6 : angle 1.22380 ( 9) SS BOND : bond 0.00205 ( 15) SS BOND : angle 0.76875 ( 30) covalent geometry : bond 0.00223 (11028) covalent geometry : angle 0.58136 (15021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 361 MET cc_start: 0.8048 (ppp) cc_final: 0.7848 (ppp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2093 time to fit residues: 16.1634 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 34 optimal weight: 0.0370 chunk 55 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.057537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.044909 restraints weight = 51090.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.045019 restraints weight = 49432.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045224 restraints weight = 51857.973| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11073 Z= 0.104 Angle : 0.639 12.755 15141 Z= 0.292 Chirality : 0.046 0.319 1953 Planarity : 0.003 0.035 1863 Dihedral : 6.715 59.123 2055 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1377 helix: 1.03 (0.24), residues: 480 sheet: -0.59 (0.31), residues: 239 loop : -1.38 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 302 HIS 0.003 0.001 HIS C 129 PHE 0.004 0.001 PHE A 350 TYR 0.011 0.001 TYR C 426 ARG 0.001 0.000 ARG B 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 15) link_NAG-ASN : angle 3.56470 ( 45) link_BETA1-4 : bond 0.00632 ( 12) link_BETA1-4 : angle 2.37250 ( 36) hydrogen bonds : bond 0.03273 ( 463) hydrogen bonds : angle 4.75782 ( 1302) link_BETA1-6 : bond 0.00323 ( 3) link_BETA1-6 : angle 1.25578 ( 9) SS BOND : bond 0.00187 ( 15) SS BOND : angle 0.53884 ( 30) covalent geometry : bond 0.00223 (11028) covalent geometry : angle 0.59847 (15021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.351 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2139 time to fit residues: 16.1997 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.057311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.045395 restraints weight = 51624.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.045096 restraints weight = 62171.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.045438 restraints weight = 67565.703| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11073 Z= 0.115 Angle : 0.674 20.353 15141 Z= 0.304 Chirality : 0.050 0.777 1953 Planarity : 0.003 0.038 1863 Dihedral : 6.712 58.117 2055 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1377 helix: 0.98 (0.24), residues: 480 sheet: -0.57 (0.31), residues: 239 loop : -1.36 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 302 HIS 0.003 0.001 HIS C 129 PHE 0.005 0.001 PHE A 350 TYR 0.011 0.001 TYR B 40 ARG 0.001 0.000 ARG C 359 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 15) link_NAG-ASN : angle 4.75347 ( 45) link_BETA1-4 : bond 0.00656 ( 12) link_BETA1-4 : angle 2.34368 ( 36) hydrogen bonds : bond 0.03374 ( 463) hydrogen bonds : angle 4.81988 ( 1302) link_BETA1-6 : bond 0.00430 ( 3) link_BETA1-6 : angle 1.21802 ( 9) SS BOND : bond 0.00201 ( 15) SS BOND : angle 0.48369 ( 30) covalent geometry : bond 0.00253 (11028) covalent geometry : angle 0.61270 (15021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1952 time to fit residues: 15.1837 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 0.0570 chunk 128 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 106 optimal weight: 0.0980 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.058197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.045468 restraints weight = 51041.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.045536 restraints weight = 50359.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.045747 restraints weight = 48903.939| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11073 Z= 0.100 Angle : 0.653 19.488 15141 Z= 0.295 Chirality : 0.048 0.624 1953 Planarity : 0.003 0.042 1863 Dihedral : 6.566 56.746 2055 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1377 helix: 1.13 (0.25), residues: 480 sheet: -0.48 (0.31), residues: 242 loop : -1.36 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 302 HIS 0.001 0.000 HIS C 129 PHE 0.004 0.001 PHE C 229 TYR 0.011 0.001 TYR C 426 ARG 0.002 0.000 ARG A 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00737 ( 15) link_NAG-ASN : angle 4.41622 ( 45) link_BETA1-4 : bond 0.00654 ( 12) link_BETA1-4 : angle 2.26851 ( 36) hydrogen bonds : bond 0.03094 ( 463) hydrogen bonds : angle 4.68691 ( 1302) link_BETA1-6 : bond 0.00432 ( 3) link_BETA1-6 : angle 1.18750 ( 9) SS BOND : bond 0.00164 ( 15) SS BOND : angle 0.47811 ( 30) covalent geometry : bond 0.00205 (11028) covalent geometry : angle 0.59760 (15021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1992 time to fit residues: 15.1169 Evaluate side-chains 42 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 106 optimal weight: 0.0040 chunk 121 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 overall best weight: 0.9112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.057339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.044891 restraints weight = 50857.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.044842 restraints weight = 52861.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045186 restraints weight = 55215.058| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11073 Z= 0.119 Angle : 0.657 19.638 15141 Z= 0.300 Chirality : 0.047 0.486 1953 Planarity : 0.003 0.043 1863 Dihedral : 6.449 55.817 2055 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.03 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1377 helix: 1.14 (0.24), residues: 479 sheet: -0.45 (0.31), residues: 242 loop : -1.34 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 302 HIS 0.003 0.001 HIS C 129 PHE 0.005 0.001 PHE A 208 TYR 0.012 0.001 TYR B 40 ARG 0.003 0.000 ARG C 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 15) link_NAG-ASN : angle 4.37105 ( 45) link_BETA1-4 : bond 0.00630 ( 12) link_BETA1-4 : angle 2.20218 ( 36) hydrogen bonds : bond 0.03268 ( 463) hydrogen bonds : angle 4.77063 ( 1302) link_BETA1-6 : bond 0.00386 ( 3) link_BETA1-6 : angle 1.17318 ( 9) SS BOND : bond 0.00211 ( 15) SS BOND : angle 0.43265 ( 30) covalent geometry : bond 0.00268 (11028) covalent geometry : angle 0.60395 (15021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.30 seconds wall clock time: 49 minutes 33.66 seconds (2973.66 seconds total)