Starting phenix.real_space_refine on Wed Mar 4 19:57:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbz_13314/03_2026/7pbz_13314.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbz_13314/03_2026/7pbz_13314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbz_13314/03_2026/7pbz_13314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbz_13314/03_2026/7pbz_13314.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbz_13314/03_2026/7pbz_13314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbz_13314/03_2026/7pbz_13314.cif" } resolution = 2.79 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 886 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 84 5.16 5 C 9650 2.51 5 N 2408 2.21 5 O 2679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14822 Number of models: 1 Model: "" Number of chains: 17 Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Chain: "A" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2695 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 319} Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2707 Classifications: {'peptide': 330} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2707 Classifications: {'peptide': 330} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2707 Classifications: {'peptide': 330} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain: "G" 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: "H" 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: "I" 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" 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: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {'HEX': 1, 'NAG': 1, 'OCT': 2, 'UND': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 1, 'ABU': 1, 'HEX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'D10': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'D10': 2, 'HEX': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.10, per 1000 atoms: 0.21 Number of scatterers: 14822 At special positions: 0 Unit cell: (91.932, 119.968, 125.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 84 16.00 O 2679 8.00 N 2408 7.00 C 9650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 483 " distance=2.04 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " 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 J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 501 " - " ASN A 111 " " NAG D 501 " - " ASN D 111 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN C 80 " " NAG J 1 " - " ASN C 149 " " NAG K 1 " - " ASN E 80 " " NAG L 1 " - " ASN E 149 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 453.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS E 267 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS C 267 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS B 267 " 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 40.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'F' and resid 474 through 478 Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'A' and resid 13 through 23 Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.645A pdb=" N ILE A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 4.415A pdb=" N VAL A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.589A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 277 removed outlier: 4.096A pdb=" N ASN A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.529A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 415 removed outlier: 3.634A pdb=" N ALA A 319 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.553A pdb=" N LYS B 13 " --> pdb=" O MET B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.532A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.303A pdb=" N ARG B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 243 removed outlier: 3.742A pdb=" N SER B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 270 Processing helix chain 'B' and resid 279 through 308 Processing helix chain 'B' and resid 420 through 429 Processing helix chain 'B' and resid 430 through 446 Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.571A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 4.118A pdb=" N ARG C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.978A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 271 Processing helix chain 'C' and resid 279 through 308 Processing helix chain 'C' and resid 420 through 446 Proline residue: C 432 - end of helix Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.365A pdb=" N ARG E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 237 removed outlier: 4.152A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 removed outlier: 3.684A pdb=" N ILE E 242 " --> pdb=" O SER E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.625A pdb=" N ARG E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 308 Processing helix chain 'E' and resid 423 through 449 Proline residue: E 435 - end of helix Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.774A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.011A pdb=" N SER D 92 " --> pdb=" O ASN D 88 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.511A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 Processing helix chain 'D' and resid 284 through 310 removed outlier: 3.521A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 417 removed outlier: 3.707A pdb=" N ALA D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.799A pdb=" N ASN D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'F' and resid 420 through 426 removed outlier: 6.652A pdb=" N MET F 421 " --> pdb=" O ALA F 437 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA F 437 " --> pdb=" O MET F 421 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP F 423 " --> pdb=" O VAL F 435 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 445 through 447 current: chain 'F' and resid 501 through 502 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 54 removed outlier: 6.540A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU A 59 " --> pdb=" O PRO A 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 71 current: chain 'A' and resid 126 through 138 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.253A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 51 removed outlier: 6.373A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 68 current: chain 'B' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.797A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 36 through 46 current: chain 'C' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.138A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 36 through 51 removed outlier: 6.394A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 68 current: chain 'E' and resid 123 through 135 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.692A pdb=" N CYS E 150 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE E 212 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR E 205 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN E 197 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG E 207 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER E 195 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER E 209 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU E 193 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER E 211 " --> pdb=" O HIS E 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS E 191 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG E 213 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 39 through 49 current: chain 'D' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.303A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR D 210 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE D 202 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 212 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER D 200 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR D 214 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL D 198 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS D 216 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN D 196 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N HIS D 218 " --> pdb=" O LEU D 194 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1671 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: 2.53 Time building geometry restraints manager: 1.47 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: 4508 1.34 - 1.46: 3892 1.46 - 1.58: 6639 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 15185 Sorted by residual: bond pdb=" CG HSM C 601 " pdb=" ND1 HSM C 601 " ideal model delta sigma weight residual 1.383 1.313 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" CD2 HSM C 601 " pdb=" NE2 HSM C 601 " ideal model delta sigma weight residual 1.376 1.314 0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" N GLN F 1 " pdb=" CA GLN F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 15180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 20305 2.88 - 5.77: 268 5.77 - 8.65: 23 8.65 - 11.54: 1 11.54 - 14.42: 1 Bond angle restraints: 20598 Sorted by residual: angle pdb=" C ALA A 316 " pdb=" N ARG A 317 " pdb=" CA ARG A 317 " ideal model delta sigma weight residual 120.28 131.67 -11.39 1.34e+00 5.57e-01 7.23e+01 angle pdb=" CA CYS E 150 " pdb=" CB CYS E 150 " pdb=" SG CYS E 150 " ideal model delta sigma weight residual 114.40 128.82 -14.42 2.30e+00 1.89e-01 3.93e+01 angle pdb=" C THR C 110 " pdb=" N VAL C 111 " pdb=" CA VAL C 111 " ideal model delta sigma weight residual 122.11 128.27 -6.16 1.12e+00 7.97e-01 3.03e+01 angle pdb=" C VAL C 109 " pdb=" N THR C 110 " pdb=" CA THR C 110 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C MET A 112 " pdb=" N THR A 113 " pdb=" CA THR A 113 " ideal model delta sigma weight residual 121.54 129.07 -7.53 1.91e+00 2.74e-01 1.55e+01 ... (remaining 20593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.34: 8705 23.34 - 46.67: 406 46.67 - 70.01: 40 70.01 - 93.35: 27 93.35 - 116.68: 26 Dihedral angle restraints: 9204 sinusoidal: 3975 harmonic: 5229 Sorted by residual: dihedral pdb=" CA LEU E 223 " pdb=" C LEU E 223 " pdb=" N GLN E 224 " pdb=" CA GLN E 224 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 156.57 23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA PRO C 276 " pdb=" C PRO C 276 " pdb=" N TYR C 277 " pdb=" CA TYR C 277 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 9201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.837: 2364 0.837 - 1.675: 6 1.675 - 2.512: 0 2.512 - 3.349: 0 3.349 - 4.186: 1 Chirality restraints: 2371 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.91e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-02 2.50e+03 2.67e+03 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-02 2.50e+03 2.48e+03 ... (remaining 2368 not shown) Planarity restraints: 2530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 111 " 0.219 2.00e-02 2.50e+03 2.14e-01 5.72e+02 pdb=" CG ASN A 111 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN A 111 " -0.083 2.00e-02 2.50e+03 pdb=" ND2 ASN A 111 " -0.319 2.00e-02 2.50e+03 pdb=" C1 NAG A 501 " 0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 149 " 0.178 2.00e-02 2.50e+03 1.90e-01 4.49e+02 pdb=" CG ASN E 149 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN E 149 " -0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN E 149 " -0.293 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.234 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 80 " 0.141 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" CG ASN C 80 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 80 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN C 80 " -0.207 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.165 2.00e-02 2.50e+03 ... (remaining 2527 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 341 2.69 - 3.24: 14249 3.24 - 3.79: 23448 3.79 - 4.35: 32448 4.35 - 4.90: 54385 Nonbonded interactions: 124871 Sorted by model distance: nonbonded pdb=" OG1 THR B 160 " pdb=" OD1 ASP B 162 " model vdw 2.136 3.040 nonbonded pdb=" O THR A 99 " pdb=" OG1 THR E 110 " model vdw 2.149 3.040 nonbonded pdb=" O THR E 233 " pdb=" OG SER E 236 " model vdw 2.168 3.040 nonbonded pdb=" OG SER E 104 " pdb=" O THR E 131 " model vdw 2.169 3.040 nonbonded pdb=" OG1 THR A 113 " pdb=" O THR B 96 " model vdw 2.182 3.040 ... (remaining 124866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 416) selection = (chain 'D' and resid 12 through 416) } ncs_group { reference = (chain 'B' and resid 8 through 447) selection = (chain 'C' and resid 8 through 447) selection = (chain 'E' and resid 8 through 450) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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: 11.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.170 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 : 0.007 0.319 15216 Z= 0.311 Angle : 1.179 48.872 20676 Z= 0.486 Chirality : 0.121 4.186 2371 Planarity : 0.006 0.143 2522 Dihedral : 15.133 116.681 5826 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.33 (0.20), residues: 1753 helix: 1.56 (0.22), residues: 587 sheet: -0.26 (0.23), residues: 454 loop : -0.49 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG E 269 TYR 0.029 0.001 TYR B 299 PHE 0.013 0.001 PHE D 298 TRP 0.007 0.001 TRP C 67 HIS 0.006 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00418 (15185) covalent geometry : angle 0.77103 (20598) SS BOND : bond 0.00407 ( 6) SS BOND : angle 1.24426 ( 12) hydrogen bonds : bond 0.12188 ( 593) hydrogen bonds : angle 5.37577 ( 1671) metal coordination : bond 0.22970 ( 3) link_ALPHA1-3 : bond 0.01180 ( 2) link_ALPHA1-3 : angle 7.40175 ( 6) link_ALPHA1-6 : bond 0.01066 ( 3) link_ALPHA1-6 : angle 19.35336 ( 9) link_BETA1-4 : bond 0.02429 ( 9) link_BETA1-4 : angle 18.48013 ( 27) link_NAG-ASN : bond 0.19261 ( 8) link_NAG-ASN : angle 12.21269 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: F 454 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7910 (mtp180) REVERT: F 465 THR cc_start: 0.8003 (p) cc_final: 0.7645 (p) REVERT: F 468 LEU cc_start: 0.7691 (tt) cc_final: 0.7317 (tt) REVERT: F 477 ASP cc_start: 0.7562 (m-30) cc_final: 0.6940 (m-30) REVERT: A 248 ASN cc_start: 0.8314 (t0) cc_final: 0.7160 (p0) REVERT: B 153 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 224 GLN cc_start: 0.8533 (mm110) cc_final: 0.8255 (mm110) REVERT: C 95 ASP cc_start: 0.7790 (t70) cc_final: 0.7423 (t0) REVERT: C 137 MET cc_start: 0.8296 (mmp) cc_final: 0.7988 (tpp) REVERT: C 283 MET cc_start: 0.8222 (mmt) cc_final: 0.8020 (mmt) REVERT: C 426 TRP cc_start: 0.7877 (t60) cc_final: 0.7430 (t60) REVERT: E 224 GLN cc_start: 0.8432 (tp40) cc_final: 0.7087 (tm-30) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.7391 time to fit residues: 189.9933 Evaluate side-chains 163 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 464 ASN F 504 GLN B 64 GLN C 113 ASN C 148 GLN E 191 HIS D 116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.059819 restraints weight = 32890.922| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.81 r_work: 0.2738 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 15216 Z= 0.285 Angle : 0.726 15.733 20676 Z= 0.357 Chirality : 0.048 0.344 2371 Planarity : 0.005 0.074 2522 Dihedral : 10.889 97.632 2500 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.53 % Allowed : 8.40 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.49 (0.20), residues: 1753 helix: 1.71 (0.21), residues: 590 sheet: -0.15 (0.23), residues: 472 loop : -0.45 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 221 TYR 0.022 0.002 TYR B 299 PHE 0.021 0.002 PHE B 293 TRP 0.009 0.001 TRP D 246 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00668 (15185) covalent geometry : angle 0.69199 (20598) SS BOND : bond 0.00391 ( 6) SS BOND : angle 1.51136 ( 12) hydrogen bonds : bond 0.04657 ( 593) hydrogen bonds : angle 4.56188 ( 1671) metal coordination : bond 0.01794 ( 3) link_ALPHA1-3 : bond 0.00565 ( 2) link_ALPHA1-3 : angle 1.76900 ( 6) link_ALPHA1-6 : bond 0.00716 ( 3) link_ALPHA1-6 : angle 2.70715 ( 9) link_BETA1-4 : bond 0.00454 ( 9) link_BETA1-4 : angle 3.33852 ( 27) link_NAG-ASN : bond 0.00655 ( 8) link_NAG-ASN : angle 5.10124 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: F 465 THR cc_start: 0.8274 (p) cc_final: 0.7794 (p) REVERT: F 467 TYR cc_start: 0.7379 (m-10) cc_final: 0.6998 (m-80) REVERT: F 477 ASP cc_start: 0.7736 (m-30) cc_final: 0.7236 (m-30) REVERT: A 213 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8121 (mmp) REVERT: B 9 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8281 (tpp) REVERT: B 224 GLN cc_start: 0.8855 (mm110) cc_final: 0.8551 (mm110) REVERT: C 95 ASP cc_start: 0.8512 (t70) cc_final: 0.7831 (t0) REVERT: C 138 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8113 (mtt) REVERT: C 275 ILE cc_start: 0.8677 (tp) cc_final: 0.8243 (pp) REVERT: C 426 TRP cc_start: 0.7814 (t60) cc_final: 0.7552 (t60) REVERT: E 179 GLU cc_start: 0.8833 (pm20) cc_final: 0.8624 (pm20) REVERT: E 224 GLN cc_start: 0.8752 (tp40) cc_final: 0.7812 (tp40) REVERT: D 63 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8383 (t70) REVERT: D 138 GLU cc_start: 0.8267 (pp20) cc_final: 0.8063 (pp20) REVERT: D 274 ARG cc_start: 0.8529 (mpt-90) cc_final: 0.8085 (mpt-90) outliers start: 24 outliers final: 9 residues processed: 182 average time/residue: 0.6727 time to fit residues: 133.3999 Evaluate side-chains 169 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN A 116 ASN B 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.079590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.061596 restraints weight = 32761.960| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.85 r_work: 0.2754 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15216 Z= 0.134 Angle : 0.600 12.436 20676 Z= 0.297 Chirality : 0.044 0.297 2371 Planarity : 0.004 0.063 2522 Dihedral : 9.487 88.536 2500 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.72 % Allowed : 10.25 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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 (0.20), residues: 1753 helix: 1.91 (0.21), residues: 591 sheet: -0.09 (0.23), residues: 454 loop : -0.41 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 180 TYR 0.026 0.001 TYR B 299 PHE 0.014 0.001 PHE B 293 TRP 0.006 0.001 TRP D 95 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00301 (15185) covalent geometry : angle 0.57475 (20598) SS BOND : bond 0.00296 ( 6) SS BOND : angle 0.96998 ( 12) hydrogen bonds : bond 0.03860 ( 593) hydrogen bonds : angle 4.31150 ( 1671) metal coordination : bond 0.01008 ( 3) link_ALPHA1-3 : bond 0.00982 ( 2) link_ALPHA1-3 : angle 1.65797 ( 6) link_ALPHA1-6 : bond 0.00807 ( 3) link_ALPHA1-6 : angle 1.92421 ( 9) link_BETA1-4 : bond 0.00394 ( 9) link_BETA1-4 : angle 2.83444 ( 27) link_NAG-ASN : bond 0.00660 ( 8) link_NAG-ASN : angle 3.83095 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.490 Fit side-chains REVERT: F 421 MET cc_start: 0.9299 (mmm) cc_final: 0.8625 (mmm) REVERT: F 465 THR cc_start: 0.8201 (p) cc_final: 0.7818 (p) REVERT: F 467 TYR cc_start: 0.7510 (m-80) cc_final: 0.7130 (m-80) REVERT: B 224 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8531 (mm110) REVERT: C 95 ASP cc_start: 0.8489 (t70) cc_final: 0.7792 (t0) REVERT: C 275 ILE cc_start: 0.8623 (tp) cc_final: 0.8263 (pp) REVERT: C 426 TRP cc_start: 0.7759 (t60) cc_final: 0.7370 (t60) REVERT: E 138 MET cc_start: 0.9120 (mtt) cc_final: 0.8866 (mtt) REVERT: D 63 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8332 (t70) REVERT: D 138 GLU cc_start: 0.8306 (pp20) cc_final: 0.8053 (pp20) REVERT: D 274 ARG cc_start: 0.8532 (mpt-90) cc_final: 0.8094 (mpt-90) outliers start: 27 outliers final: 11 residues processed: 175 average time/residue: 0.6741 time to fit residues: 128.4140 Evaluate side-chains 163 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN ** E 224 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 = 0.3263 r_free = 0.3263 target = 0.079252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.061284 restraints weight = 32759.782| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.85 r_work: 0.2762 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15216 Z= 0.146 Angle : 0.585 11.537 20676 Z= 0.292 Chirality : 0.044 0.302 2371 Planarity : 0.004 0.056 2522 Dihedral : 8.987 89.373 2500 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.72 % Allowed : 11.78 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.74 (0.20), residues: 1753 helix: 2.03 (0.21), residues: 591 sheet: -0.03 (0.23), residues: 454 loop : -0.40 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 274 TYR 0.025 0.001 TYR B 299 PHE 0.014 0.001 PHE B 293 TRP 0.007 0.001 TRP F 502 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00335 (15185) covalent geometry : angle 0.56376 (20598) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.95370 ( 12) hydrogen bonds : bond 0.03698 ( 593) hydrogen bonds : angle 4.24055 ( 1671) metal coordination : bond 0.00477 ( 3) link_ALPHA1-3 : bond 0.00993 ( 2) link_ALPHA1-3 : angle 1.83690 ( 6) link_ALPHA1-6 : bond 0.00841 ( 3) link_ALPHA1-6 : angle 2.04643 ( 9) link_BETA1-4 : bond 0.00390 ( 9) link_BETA1-4 : angle 2.59845 ( 27) link_NAG-ASN : bond 0.00601 ( 8) link_NAG-ASN : angle 3.36137 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.512 Fit side-chains REVERT: F 465 THR cc_start: 0.8129 (p) cc_final: 0.7796 (p) REVERT: F 467 TYR cc_start: 0.7561 (m-80) cc_final: 0.7141 (m-80) REVERT: F 504 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: B 14 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: B 224 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8547 (mm110) REVERT: C 95 ASP cc_start: 0.8514 (t70) cc_final: 0.7757 (t0) REVERT: C 275 ILE cc_start: 0.8604 (tp) cc_final: 0.8259 (pp) REVERT: C 426 TRP cc_start: 0.7762 (t60) cc_final: 0.7391 (t60) REVERT: E 224 GLN cc_start: 0.8893 (tp40) cc_final: 0.8008 (tm-30) REVERT: D 138 GLU cc_start: 0.8313 (pp20) cc_final: 0.8034 (pp20) outliers start: 27 outliers final: 14 residues processed: 173 average time/residue: 0.6242 time to fit residues: 118.2429 Evaluate side-chains 166 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 145 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN A 116 ASN ** E 224 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 = 0.3208 r_free = 0.3208 target = 0.076609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.058875 restraints weight = 33177.920| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.88 r_work: 0.2692 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15216 Z= 0.252 Angle : 0.646 11.269 20676 Z= 0.322 Chirality : 0.046 0.340 2371 Planarity : 0.004 0.057 2522 Dihedral : 8.668 86.353 2500 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.23 % Allowed : 13.11 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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 (0.20), residues: 1753 helix: 2.03 (0.21), residues: 593 sheet: -0.08 (0.23), residues: 471 loop : -0.44 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 274 TYR 0.027 0.002 TYR B 299 PHE 0.016 0.002 PHE A 304 TRP 0.009 0.001 TRP D 412 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00588 (15185) covalent geometry : angle 0.62745 (20598) SS BOND : bond 0.00363 ( 6) SS BOND : angle 1.51794 ( 12) hydrogen bonds : bond 0.04235 ( 593) hydrogen bonds : angle 4.33298 ( 1671) metal coordination : bond 0.00445 ( 3) link_ALPHA1-3 : bond 0.00757 ( 2) link_ALPHA1-3 : angle 2.09209 ( 6) link_ALPHA1-6 : bond 0.00897 ( 3) link_ALPHA1-6 : angle 2.12121 ( 9) link_BETA1-4 : bond 0.00380 ( 9) link_BETA1-4 : angle 2.67955 ( 27) link_NAG-ASN : bond 0.00582 ( 8) link_NAG-ASN : angle 3.15038 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: F 465 THR cc_start: 0.8177 (p) cc_final: 0.7856 (p) REVERT: F 477 ASP cc_start: 0.7752 (m-30) cc_final: 0.7504 (m-30) REVERT: F 504 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: B 9 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8238 (tpp) REVERT: B 14 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: B 224 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8702 (mm110) REVERT: C 275 ILE cc_start: 0.8653 (tp) cc_final: 0.8425 (pp) REVERT: E 224 GLN cc_start: 0.8772 (tp40) cc_final: 0.8545 (tp-100) REVERT: D 138 GLU cc_start: 0.8409 (pp20) cc_final: 0.8142 (pp20) REVERT: D 274 ARG cc_start: 0.8406 (mpt-90) cc_final: 0.8116 (mpt-90) outliers start: 35 outliers final: 17 residues processed: 178 average time/residue: 0.6421 time to fit residues: 124.8040 Evaluate side-chains 169 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 164 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN B 439 ASN ** E 224 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 = 0.3232 r_free = 0.3232 target = 0.077854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.060158 restraints weight = 32973.590| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.89 r_work: 0.2723 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15216 Z= 0.157 Angle : 0.602 10.522 20676 Z= 0.297 Chirality : 0.044 0.303 2371 Planarity : 0.004 0.054 2522 Dihedral : 8.179 83.190 2500 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.16 % Allowed : 14.00 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.80 (0.20), residues: 1753 helix: 2.10 (0.21), residues: 595 sheet: -0.06 (0.23), residues: 469 loop : -0.36 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 274 TYR 0.026 0.001 TYR B 299 PHE 0.023 0.001 PHE C 306 TRP 0.008 0.001 TRP D 412 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00359 (15185) covalent geometry : angle 0.58483 (20598) SS BOND : bond 0.00352 ( 6) SS BOND : angle 1.12387 ( 12) hydrogen bonds : bond 0.03702 ( 593) hydrogen bonds : angle 4.19550 ( 1671) metal coordination : bond 0.00394 ( 3) link_ALPHA1-3 : bond 0.01010 ( 2) link_ALPHA1-3 : angle 1.86914 ( 6) link_ALPHA1-6 : bond 0.01001 ( 3) link_ALPHA1-6 : angle 2.09178 ( 9) link_BETA1-4 : bond 0.00446 ( 9) link_BETA1-4 : angle 2.27697 ( 27) link_NAG-ASN : bond 0.00608 ( 8) link_NAG-ASN : angle 3.08541 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: F 6 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5768 (mp0) REVERT: F 463 LYS cc_start: 0.8692 (tptp) cc_final: 0.8291 (tptp) REVERT: F 465 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7860 (p) REVERT: F 477 ASP cc_start: 0.7580 (m-30) cc_final: 0.7102 (m-30) REVERT: F 504 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: A 242 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8605 (mt0) REVERT: A 274 ARG cc_start: 0.8092 (tpp-160) cc_final: 0.7493 (tpp-160) REVERT: B 14 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: B 49 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7125 (tmm) REVERT: B 224 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8580 (mm110) REVERT: C 165 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7599 (tm-30) REVERT: C 275 ILE cc_start: 0.8627 (tp) cc_final: 0.8409 (pp) REVERT: E 224 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8568 (tp-100) REVERT: D 63 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8351 (t70) REVERT: D 138 GLU cc_start: 0.8415 (pp20) cc_final: 0.8140 (pp20) REVERT: D 274 ARG cc_start: 0.8361 (mpt-90) cc_final: 0.8068 (mpt-90) outliers start: 34 outliers final: 11 residues processed: 174 average time/residue: 0.6532 time to fit residues: 123.8281 Evaluate side-chains 169 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN A 275 ASN A 308 ASN ** E 224 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 = 0.3246 r_free = 0.3246 target = 0.078597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.060931 restraints weight = 32496.199| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.88 r_work: 0.2741 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15216 Z= 0.128 Angle : 0.585 10.620 20676 Z= 0.290 Chirality : 0.044 0.304 2371 Planarity : 0.004 0.052 2522 Dihedral : 7.762 79.708 2500 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.78 % Allowed : 14.89 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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 (0.20), residues: 1753 helix: 2.15 (0.21), residues: 596 sheet: -0.03 (0.24), residues: 454 loop : -0.34 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 454 TYR 0.026 0.001 TYR B 299 PHE 0.021 0.001 PHE C 306 TRP 0.007 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00291 (15185) covalent geometry : angle 0.57018 (20598) SS BOND : bond 0.00261 ( 6) SS BOND : angle 0.89450 ( 12) hydrogen bonds : bond 0.03442 ( 593) hydrogen bonds : angle 4.10663 ( 1671) metal coordination : bond 0.00541 ( 3) link_ALPHA1-3 : bond 0.01057 ( 2) link_ALPHA1-3 : angle 1.80112 ( 6) link_ALPHA1-6 : bond 0.01095 ( 3) link_ALPHA1-6 : angle 2.13217 ( 9) link_BETA1-4 : bond 0.00484 ( 9) link_BETA1-4 : angle 2.12315 ( 27) link_NAG-ASN : bond 0.00549 ( 8) link_NAG-ASN : angle 2.86030 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: F 463 LYS cc_start: 0.8770 (tptp) cc_final: 0.8415 (tptp) REVERT: F 465 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7890 (p) REVERT: F 477 ASP cc_start: 0.7512 (m-30) cc_final: 0.7279 (m-30) REVERT: B 14 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: B 49 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7191 (tmm) REVERT: B 224 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8574 (mm110) REVERT: C 138 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8290 (mtt) REVERT: C 165 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 275 ILE cc_start: 0.8554 (tp) cc_final: 0.8343 (pp) REVERT: E 224 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: D 138 GLU cc_start: 0.8403 (pp20) cc_final: 0.8136 (pp20) outliers start: 28 outliers final: 12 residues processed: 175 average time/residue: 0.6530 time to fit residues: 124.7749 Evaluate side-chains 169 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN C 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.077226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.059553 restraints weight = 33023.814| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.88 r_work: 0.2706 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15216 Z= 0.196 Angle : 0.618 10.832 20676 Z= 0.306 Chirality : 0.045 0.318 2371 Planarity : 0.004 0.052 2522 Dihedral : 7.682 77.551 2500 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.97 % Allowed : 15.02 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.81 (0.20), residues: 1753 helix: 2.11 (0.21), residues: 596 sheet: -0.05 (0.23), residues: 470 loop : -0.36 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 274 TYR 0.027 0.001 TYR B 299 PHE 0.017 0.001 PHE C 306 TRP 0.009 0.001 TRP C 67 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00456 (15185) covalent geometry : angle 0.60096 (20598) SS BOND : bond 0.00320 ( 6) SS BOND : angle 1.27776 ( 12) hydrogen bonds : bond 0.03813 ( 593) hydrogen bonds : angle 4.15341 ( 1671) metal coordination : bond 0.00154 ( 3) link_ALPHA1-3 : bond 0.00938 ( 2) link_ALPHA1-3 : angle 1.91571 ( 6) link_ALPHA1-6 : bond 0.01029 ( 3) link_ALPHA1-6 : angle 2.17950 ( 9) link_BETA1-4 : bond 0.00420 ( 9) link_BETA1-4 : angle 2.23661 ( 27) link_NAG-ASN : bond 0.00528 ( 8) link_NAG-ASN : angle 3.09082 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 455 PHE cc_start: 0.8079 (m-80) cc_final: 0.7736 (m-80) REVERT: F 465 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8075 (p) REVERT: F 467 TYR cc_start: 0.8102 (m-80) cc_final: 0.7601 (m-80) REVERT: F 469 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8143 (mp0) REVERT: F 477 ASP cc_start: 0.7548 (m-30) cc_final: 0.7339 (m-30) REVERT: F 504 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: B 14 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: B 49 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7245 (tmm) REVERT: B 224 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8698 (mm110) REVERT: C 49 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7671 (ppp) REVERT: C 138 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8406 (mtt) REVERT: C 275 ILE cc_start: 0.8573 (tp) cc_final: 0.8344 (pp) REVERT: C 301 PHE cc_start: 0.8026 (t80) cc_final: 0.7571 (t80) REVERT: E 224 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: D 138 GLU cc_start: 0.8403 (pp20) cc_final: 0.8135 (pp20) outliers start: 31 outliers final: 13 residues processed: 170 average time/residue: 0.6399 time to fit residues: 118.9367 Evaluate side-chains 171 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 141 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 119 optimal weight: 0.0050 chunk 58 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN A 275 ASN C 303 ASN ** E 224 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 = 0.3235 r_free = 0.3235 target = 0.078042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.060357 restraints weight = 32832.034| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.88 r_work: 0.2713 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15216 Z= 0.140 Angle : 0.597 10.627 20676 Z= 0.296 Chirality : 0.044 0.302 2371 Planarity : 0.004 0.050 2522 Dihedral : 7.521 75.183 2500 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.46 % Allowed : 15.98 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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 (0.20), residues: 1753 helix: 2.17 (0.21), residues: 596 sheet: -0.03 (0.23), residues: 470 loop : -0.33 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 269 TYR 0.026 0.001 TYR B 299 PHE 0.016 0.001 PHE C 306 TRP 0.007 0.001 TRP D 412 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00319 (15185) covalent geometry : angle 0.58238 (20598) SS BOND : bond 0.00266 ( 6) SS BOND : angle 1.01024 ( 12) hydrogen bonds : bond 0.03548 ( 593) hydrogen bonds : angle 4.09414 ( 1671) metal coordination : bond 0.00423 ( 3) link_ALPHA1-3 : bond 0.01008 ( 2) link_ALPHA1-3 : angle 1.70795 ( 6) link_ALPHA1-6 : bond 0.01116 ( 3) link_ALPHA1-6 : angle 2.19352 ( 9) link_BETA1-4 : bond 0.00480 ( 9) link_BETA1-4 : angle 2.05435 ( 27) link_NAG-ASN : bond 0.00534 ( 8) link_NAG-ASN : angle 2.92306 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 3 GLN cc_start: 0.8742 (mp10) cc_final: 0.8521 (mm-40) REVERT: F 455 PHE cc_start: 0.8006 (m-80) cc_final: 0.7629 (m-80) REVERT: F 465 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7962 (p) REVERT: F 467 TYR cc_start: 0.8106 (m-80) cc_final: 0.7580 (m-80) REVERT: F 477 ASP cc_start: 0.7607 (m-30) cc_final: 0.7380 (m-30) REVERT: F 504 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: B 14 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: B 49 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7263 (tmm) REVERT: B 224 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8611 (mm110) REVERT: C 138 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8363 (mtt) REVERT: C 275 ILE cc_start: 0.8485 (tp) cc_final: 0.8227 (pp) REVERT: C 301 PHE cc_start: 0.8007 (t80) cc_final: 0.7589 (t80) REVERT: E 224 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8472 (tp-100) REVERT: D 138 GLU cc_start: 0.8427 (pp20) cc_final: 0.8159 (pp20) REVERT: D 229 GLN cc_start: 0.8534 (tp40) cc_final: 0.8213 (tt0) outliers start: 23 outliers final: 12 residues processed: 170 average time/residue: 0.6547 time to fit residues: 121.5212 Evaluate side-chains 170 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 63 optimal weight: 0.2980 chunk 153 optimal weight: 0.6980 chunk 46 optimal weight: 0.0980 chunk 161 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN C 303 ASN ** E 224 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 = 0.3255 r_free = 0.3255 target = 0.079174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.061419 restraints weight = 32684.158| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.90 r_work: 0.2758 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15216 Z= 0.110 Angle : 0.590 10.972 20676 Z= 0.292 Chirality : 0.043 0.300 2371 Planarity : 0.004 0.051 2522 Dihedral : 7.240 69.441 2500 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.34 % Allowed : 16.36 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.97 (0.21), residues: 1753 helix: 2.23 (0.21), residues: 596 sheet: 0.08 (0.24), residues: 461 loop : -0.29 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 180 TYR 0.025 0.001 TYR B 299 PHE 0.019 0.001 PHE B 301 TRP 0.006 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00243 (15185) covalent geometry : angle 0.57687 (20598) SS BOND : bond 0.00212 ( 6) SS BOND : angle 0.76969 ( 12) hydrogen bonds : bond 0.03243 ( 593) hydrogen bonds : angle 4.01257 ( 1671) metal coordination : bond 0.00549 ( 3) link_ALPHA1-3 : bond 0.01037 ( 2) link_ALPHA1-3 : angle 1.55967 ( 6) link_ALPHA1-6 : bond 0.01111 ( 3) link_ALPHA1-6 : angle 2.14118 ( 9) link_BETA1-4 : bond 0.00541 ( 9) link_BETA1-4 : angle 1.89273 ( 27) link_NAG-ASN : bond 0.00576 ( 8) link_NAG-ASN : angle 2.75455 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: F 3 GLN cc_start: 0.8747 (mp10) cc_final: 0.8525 (mm-40) REVERT: F 444 SER cc_start: 0.8722 (t) cc_final: 0.8072 (p) REVERT: F 455 PHE cc_start: 0.7959 (m-80) cc_final: 0.7622 (m-80) REVERT: F 463 LYS cc_start: 0.8434 (tptp) cc_final: 0.8138 (tptp) REVERT: F 477 ASP cc_start: 0.7641 (m-30) cc_final: 0.7356 (m-30) REVERT: F 504 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: A 114 MET cc_start: 0.8319 (mmm) cc_final: 0.8104 (mmp) REVERT: B 14 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: B 49 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7355 (tmm) REVERT: B 224 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8551 (mm110) REVERT: C 138 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: C 165 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 301 PHE cc_start: 0.7987 (t80) cc_final: 0.7570 (t80) REVERT: E 224 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8383 (tp-100) REVERT: D 138 GLU cc_start: 0.8417 (pp20) cc_final: 0.8143 (pp20) REVERT: D 229 GLN cc_start: 0.8453 (tp40) cc_final: 0.8149 (tt0) outliers start: 21 outliers final: 12 residues processed: 171 average time/residue: 0.6329 time to fit residues: 118.4579 Evaluate side-chains 168 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.0370 chunk 56 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 28 optimal weight: 0.0060 chunk 147 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 160 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN C 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.079463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.061811 restraints weight = 32528.076| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.89 r_work: 0.2749 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15216 Z= 0.111 Angle : 0.584 10.594 20676 Z= 0.289 Chirality : 0.043 0.300 2371 Planarity : 0.004 0.047 2522 Dihedral : 7.035 60.403 2500 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.40 % Allowed : 15.98 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 1.01 (0.21), residues: 1753 helix: 2.26 (0.21), residues: 596 sheet: 0.10 (0.24), residues: 470 loop : -0.26 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 180 TYR 0.025 0.001 TYR B 299 PHE 0.013 0.001 PHE C 306 TRP 0.007 0.001 TRP C 237 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00248 (15185) covalent geometry : angle 0.57084 (20598) SS BOND : bond 0.00213 ( 6) SS BOND : angle 0.78240 ( 12) hydrogen bonds : bond 0.03167 ( 593) hydrogen bonds : angle 3.96742 ( 1671) metal coordination : bond 0.00481 ( 3) link_ALPHA1-3 : bond 0.01017 ( 2) link_ALPHA1-3 : angle 1.54716 ( 6) link_ALPHA1-6 : bond 0.01258 ( 3) link_ALPHA1-6 : angle 2.15100 ( 9) link_BETA1-4 : bond 0.00544 ( 9) link_BETA1-4 : angle 1.85359 ( 27) link_NAG-ASN : bond 0.00564 ( 8) link_NAG-ASN : angle 2.70672 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4323.41 seconds wall clock time: 74 minutes 34.95 seconds (4474.95 seconds total)