Starting phenix.real_space_refine on Fri Jul 3 09:23:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5bkg_9404/07_2026/5bkg_9404.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkg_9404/07_2026/5bkg_9404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5bkg_9404/07_2026/5bkg_9404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkg_9404/07_2026/5bkg_9404.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5bkg_9404/07_2026/5bkg_9404.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5bkg_9404/07_2026/5bkg_9404.cif" model { file = "/net/cci-nas-00/data/ceres_data/5bkg_9404/07_2026/5bkg_9404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkg_9404/07_2026/5bkg_9404.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 8815 2.51 5 N 2151 2.21 5 O 2456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13509 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2677 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2676 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2681 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2676 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2658 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {'NAG': 2} Inner-chain residues flagged as termini: ['pdbres="GLY B 503 "'] Classifications: {'peptide': 2, 'undetermined': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="NAG B 501 " pdbres="NAG B 502 " Not linked: pdbres="NAG B 502 " pdbres="GLY B 503 " Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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 chiralities: 2 Chain: "D" 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 chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.26, per 1000 atoms: 0.24 Number of scatterers: 13509 At special positions: 0 Unit cell: (88.81, 88.81, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2456 8.00 N 2151 7.00 C 8815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 205 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " 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 NAG-ASN " NAG A 501 " - " ASN A 45 " " NAG A 502 " - " ASN A 76 " " NAG B 501 " - " ASN B 45 " " NAG B 502 " - " ASN B 76 " " NAG C 501 " - " ASN C 45 " " NAG C 502 " - " ASN C 76 " " NAG D 501 " - " ASN D 45 " " NAG D 502 " - " ASN D 76 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 564.8 milliseconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 21 sheets defined 38.5% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.613A pdb=" N GLY A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 93 through 100 removed outlier: 4.096A pdb=" N ASP A 98 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.921A pdb=" N ARG A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 315 Processing helix chain 'A' and resid 384 through 415 Proline residue: A 400 - end of helix Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 93 through 100 removed outlier: 3.590A pdb=" N MET B 96 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP B 98 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 234 through 250 Processing helix chain 'B' and resid 255 through 280 Processing helix chain 'B' and resid 288 through 316 removed outlier: 3.677A pdb=" N ARG B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 416 Proline residue: B 400 - end of helix removed outlier: 3.591A pdb=" N ILE B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 93 through 100 removed outlier: 3.554A pdb=" N ASP C 98 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 100 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 removed outlier: 4.465A pdb=" N ASN C 151 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 234 through 247 Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 255 through 280 Processing helix chain 'C' and resid 288 through 316 Processing helix chain 'C' and resid 384 through 415 Proline residue: C 400 - end of helix Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 78 through 81 Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.893A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP D 98 " --> pdb=" O PRO D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 234 through 246 Processing helix chain 'D' and resid 246 through 251 removed outlier: 4.065A pdb=" N TRP D 250 " --> pdb=" O TRP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 280 removed outlier: 3.576A pdb=" N ARG D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 315 Processing helix chain 'D' and resid 384 through 415 Proline residue: D 400 - end of helix Processing helix chain 'E' and resid 31 through 39 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 251 through 265 removed outlier: 3.523A pdb=" N TRP E 263 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 275 through 297 removed outlier: 4.407A pdb=" N LEU E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 332 Processing helix chain 'E' and resid 448 through 475 Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 4.516A pdb=" N LEU A 125 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP A 64 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER A 57 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG A 66 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE A 55 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN A 68 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 51 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 44 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU A 176 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 46 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 removed outlier: 4.184A pdb=" N GLY A 112 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP A 64 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER A 57 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG A 66 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE A 55 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN A 68 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 51 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N GLN A 184 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 50 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 114 removed outlier: 6.011A pdb=" N GLU B 110 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER B 144 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY B 112 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP B 64 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 58 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 54 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 70 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE B 52 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 72 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE B 50 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLN B 74 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N CYS B 48 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ASN B 76 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL B 46 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 123 through 126 removed outlier: 6.728A pdb=" N ASP B 64 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 58 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 54 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 70 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE B 52 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 72 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE B 50 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLN B 74 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N CYS B 48 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ASN B 76 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL B 46 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N GLN B 184 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 50 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AA8, first strand: chain 'B' and resid 156 through 161 removed outlier: 3.807A pdb=" N GLU B 224 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 161 Processing sheet with id=AB1, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.900A pdb=" N LYS C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG C 66 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 55 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN C 68 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE C 51 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN C 76 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN C 45 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL C 44 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLU C 176 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL C 46 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 110 through 114 removed outlier: 6.261A pdb=" N GLU C 110 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER C 144 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY C 112 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG C 66 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 55 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN C 68 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE C 51 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN C 76 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN C 45 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N GLN C 184 " --> pdb=" O CYS C 48 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE C 50 " --> pdb=" O GLN C 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 105 through 107 Processing sheet with id=AB4, first strand: chain 'C' and resid 105 through 107 Processing sheet with id=AB5, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.832A pdb=" N LYS D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP D 64 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL D 58 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN D 68 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 54 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE D 70 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE D 52 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG D 72 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE D 50 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLN D 74 " --> pdb=" O CYS D 48 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N CYS D 48 " --> pdb=" O GLN D 74 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN D 76 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL D 46 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 110 through 114 removed outlier: 6.174A pdb=" N GLU D 110 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER D 144 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY D 112 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP D 64 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL D 58 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN D 68 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 54 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE D 70 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE D 52 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG D 72 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE D 50 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLN D 74 " --> pdb=" O CYS D 48 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N CYS D 48 " --> pdb=" O GLN D 74 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN D 76 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL D 46 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N GLN D 184 " --> pdb=" O CYS D 48 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE D 50 " --> pdb=" O GLN D 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 156 through 157 removed outlier: 3.655A pdb=" N LEU D 223 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 160 through 163 Processing sheet with id=AB9, first strand: chain 'E' and resid 126 through 128 removed outlier: 5.988A pdb=" N GLU E 126 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER E 160 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 128 " --> pdb=" O THR E 158 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 85 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 139 through 143 removed outlier: 3.572A pdb=" N LEU E 85 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 121 through 123 Processing sheet with id=AC3, first strand: chain 'E' and resid 224 through 225 779 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.51 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: 4134 1.34 - 1.46: 3494 1.46 - 1.58: 6075 1.58 - 1.70: 0 1.70 - 1.83: 142 Bond restraints: 13845 Sorted by residual: bond pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.78e+00 bond pdb=" N VAL C 58 " pdb=" CA VAL C 58 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.05e+00 bond pdb=" N ARG B 72 " pdb=" CA ARG B 72 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.26e-02 6.30e+03 7.03e+00 bond pdb=" N PHE A 214 " pdb=" CA PHE A 214 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.22e-02 6.72e+03 6.56e+00 bond pdb=" N PHE B 166 " pdb=" CA PHE B 166 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.17e-02 7.31e+03 6.50e+00 ... (remaining 13840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 17983 1.17 - 2.33: 666 2.33 - 3.50: 129 3.50 - 4.67: 44 4.67 - 5.84: 13 Bond angle restraints: 18835 Sorted by residual: angle pdb=" O VAL D 44 " pdb=" C VAL D 44 " pdb=" N ASN D 45 " ideal model delta sigma weight residual 122.93 118.28 4.65 1.06e+00 8.90e-01 1.93e+01 angle pdb=" C ASN D 45 " pdb=" N VAL D 46 " pdb=" CA VAL D 46 " ideal model delta sigma weight residual 121.66 126.98 -5.32 1.38e+00 5.25e-01 1.49e+01 angle pdb=" CA VAL E 277 " pdb=" C VAL E 277 " pdb=" N PRO E 278 " ideal model delta sigma weight residual 120.83 118.49 2.34 6.10e-01 2.69e+00 1.47e+01 angle pdb=" CA PHE B 70 " pdb=" C PHE B 70 " pdb=" O PHE B 70 " ideal model delta sigma weight residual 122.37 118.16 4.21 1.15e+00 7.56e-01 1.34e+01 angle pdb=" C ASN D 45 " pdb=" CA ASN D 45 " pdb=" CB ASN D 45 " ideal model delta sigma weight residual 111.41 116.70 -5.29 1.70e+00 3.46e-01 9.70e+00 ... (remaining 18830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7460 17.71 - 35.41: 579 35.41 - 53.12: 74 53.12 - 70.83: 6 70.83 - 88.53: 8 Dihedral angle restraints: 8127 sinusoidal: 3142 harmonic: 4985 Sorted by residual: dihedral pdb=" CB CYS E 221 " pdb=" SG CYS E 221 " pdb=" SG CYS E 233 " pdb=" CB CYS E 233 " ideal model delta sinusoidal sigma weight residual 93.00 -178.47 -88.53 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual 93.00 50.10 42.90 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CB CYS B 145 " pdb=" SG CYS B 145 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual 93.00 51.36 41.64 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 8124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2139 0.106 - 0.213: 38 0.213 - 0.319: 4 0.319 - 0.425: 1 0.425 - 0.532: 1 Chirality restraints: 2183 Sorted by residual: chirality pdb=" C1 NAG C 502 " pdb=" ND2 ASN C 76 " pdb=" C2 NAG C 502 " pdb=" O5 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 45 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA PHE C 70 " pdb=" N PHE C 70 " pdb=" C PHE C 70 " pdb=" CB PHE C 70 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2180 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " -0.190 2.00e-02 2.50e+03 1.58e-01 3.13e+02 pdb=" C7 NAG D 501 " 0.051 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " -0.138 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " 0.258 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 69 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE C 69 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE C 69 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE C 70 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 44 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" C VAL D 44 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL D 44 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN D 45 " 0.014 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 188 2.62 - 3.19: 12877 3.19 - 3.76: 19865 3.76 - 4.33: 28309 4.33 - 4.90: 47052 Nonbonded interactions: 108291 Sorted by model distance: nonbonded pdb=" O THR B 119 " pdb=" OG1 THR B 120 " model vdw 2.044 3.040 nonbonded pdb=" O THR A 119 " pdb=" OG1 THR A 120 " model vdw 2.097 3.040 nonbonded pdb=" O VAL C 118 " pdb=" OG1 THR C 119 " model vdw 2.105 3.040 nonbonded pdb=" O THR C 119 " pdb=" OG1 THR C 120 " model vdw 2.108 3.040 nonbonded pdb=" O VAL B 118 " pdb=" OG1 THR B 119 " model vdw 2.115 3.040 ... (remaining 108286 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 15 through 243 or (resid 244 and (name N or name CA or nam \ e C or name O or name CB )) or resid 245 through 384 or (resid 385 through 390 a \ nd (name N or name CA or name C or name O or name CB )) or resid 391 or (resid 3 \ 92 through 398 and (name N or name CA or name C or name O or name CB )) or resid \ 399 through 502)) selection = (chain 'B' and (resid 15 through 316 or (resid 383 through 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 through 417 or (resid 418 a \ nd (name N or name CA or name C or name O or name CB )) or resid 501 through 502 \ )) selection = (chain 'C' and (resid 15 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 198 or (resid 199 and (name N or n \ ame CA or name C or name O or name CB )) or resid 200 through 243 or (resid 244 \ and (name N or name CA or name C or name O or name CB )) or resid 245 through 38 \ 6 or (resid 387 through 390 and (name N or name CA or name C or name O or name C \ B )) or resid 391 through 392 or (resid 393 through 398 and (name N or name CA o \ r name C or name O or name CB )) or resid 399 through 502)) selection = (chain 'D' and (resid 15 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 243 or (resid 244 and (name N or n \ ame CA or name C or name O or name CB )) or resid 245 through 385 or (resid 386 \ through 390 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 1 through 392 or (resid 393 through 398 and (name N or name CA or name C or name \ O or name CB )) or resid 399 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.640 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.004 0.063 13862 Z= 0.213 Angle : 0.599 10.008 18878 Z= 0.335 Chirality : 0.045 0.532 2183 Planarity : 0.005 0.158 2335 Dihedral : 12.344 83.193 4869 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.21 % Allowed : 3.51 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.60 (0.18), residues: 1666 helix: -1.02 (0.19), residues: 594 sheet: -3.00 (0.22), residues: 418 loop : -3.14 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 154 TYR 0.018 0.001 TYR B 308 PHE 0.021 0.001 PHE A 406 TRP 0.008 0.001 TRP D 75 HIS 0.002 0.001 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (13845) covalent geometry : angle 0.57943 / 0.33 (18835) SS BOND : bond 0.00369 / 0.20 ( 8) SS BOND : angle 2.10199 / 0.90 ( 16) hydrogen bonds : bond 0.10864 / 7.22 ( 670) hydrogen bonds : angle 6.64399 / 4.48 ( 2256) link_NAG-ASN : bond 0.00689 / 0.36 ( 9) link_NAG-ASN : angle 3.77092 / 2.04 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 279 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7128 (p0) cc_final: 0.6907 (p0) REVERT: A 157 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7029 (mm-40) REVERT: C 109 ASN cc_start: 0.8583 (p0) cc_final: 0.8167 (p0) REVERT: D 68 ASN cc_start: 0.7620 (p0) cc_final: 0.7375 (p0) REVERT: D 117 ASP cc_start: 0.6900 (p0) cc_final: 0.6637 (p0) REVERT: E 125 ASN cc_start: 0.8419 (p0) cc_final: 0.7784 (p0) REVERT: E 237 ILE cc_start: 0.9033 (mt) cc_final: 0.8756 (mt) REVERT: E 449 LYS cc_start: 0.7935 (tttt) cc_final: 0.7627 (ttpt) outliers start: 3 outliers final: 0 residues processed: 281 average time/residue: 0.1081 time to fit residues: 45.6359 Evaluate side-chains 185 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.0030 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 ASN B 222 HIS B 312 ASN C 73 GLN C 184 GLN C 208 HIS C 312 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.137702 restraints weight = 18483.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140534 restraints weight = 10929.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142410 restraints weight = 7508.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143448 restraints weight = 5741.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144343 restraints weight = 4830.274| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13862 Z= 0.145 Angle : 0.662 13.226 18878 Z= 0.326 Chirality : 0.046 0.416 2183 Planarity : 0.004 0.047 2335 Dihedral : 5.124 80.537 1816 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.65 % Allowed : 12.16 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.20), residues: 1666 helix: 0.49 (0.21), residues: 602 sheet: -2.31 (0.26), residues: 350 loop : -2.36 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 66 TYR 0.017 0.001 TYR C 308 PHE 0.017 0.002 PHE D 313 TRP 0.009 0.001 TRP E 267 HIS 0.007 0.001 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (13845) covalent geometry : angle 0.63378 / 0.32 (18835) SS BOND : bond 0.00420 / 0.21 ( 8) SS BOND : angle 2.09180 / 0.84 ( 16) hydrogen bonds : bond 0.03879 / 2.53 ( 670) hydrogen bonds : angle 4.87271 / 3.32 ( 2256) link_NAG-ASN : bond 0.00915 / 0.50 ( 9) link_NAG-ASN : angle 4.90517 / 2.33 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7124 (mm-40) REVERT: A 294 MET cc_start: 0.8080 (mmm) cc_final: 0.7876 (mmm) REVERT: A 415 LYS cc_start: 0.8050 (tppp) cc_final: 0.7789 (ttpt) REVERT: B 246 TRP cc_start: 0.8156 (m-10) cc_final: 0.7704 (m-10) REVERT: C 64 ASP cc_start: 0.8114 (p0) cc_final: 0.7891 (p0) REVERT: C 109 ASN cc_start: 0.8681 (p0) cc_final: 0.8345 (p0) REVERT: C 250 TRP cc_start: 0.7878 (m100) cc_final: 0.7635 (m100) REVERT: C 270 MET cc_start: 0.8646 (tpp) cc_final: 0.7523 (tpp) REVERT: C 308 TYR cc_start: 0.8236 (t80) cc_final: 0.7671 (t80) REVERT: D 68 ASN cc_start: 0.8218 (p0) cc_final: 0.7994 (p0) REVERT: D 259 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6713 (mtp180) REVERT: E 174 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.7049 (mtp85) REVERT: E 237 ILE cc_start: 0.8887 (mt) cc_final: 0.8615 (mt) outliers start: 24 outliers final: 17 residues processed: 226 average time/residue: 0.1080 time to fit residues: 36.9172 Evaluate side-chains 190 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 281 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 116 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 208 HIS B 312 ASN C 68 ASN C 208 HIS ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128348 restraints weight = 18754.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131209 restraints weight = 10890.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133160 restraints weight = 7408.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134409 restraints weight = 5609.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135067 restraints weight = 4627.042| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13862 Z= 0.204 Angle : 0.666 12.088 18878 Z= 0.328 Chirality : 0.046 0.476 2183 Planarity : 0.004 0.041 2335 Dihedral : 5.210 76.576 1816 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.44 % Allowed : 14.36 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.35 (0.21), residues: 1666 helix: 1.14 (0.21), residues: 574 sheet: -1.97 (0.27), residues: 355 loop : -1.99 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 36 TYR 0.026 0.002 TYR E 325 PHE 0.019 0.002 PHE C 70 TRP 0.009 0.001 TRP B 177 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (13845) covalent geometry : angle 0.64224 / 0.32 (18835) SS BOND : bond 0.00315 / 0.18 ( 8) SS BOND : angle 1.90097 / 0.73 ( 16) hydrogen bonds : bond 0.03957 / 2.59 ( 670) hydrogen bonds : angle 4.72356 / 3.22 ( 2256) link_NAG-ASN : bond 0.00787 / 0.44 ( 9) link_NAG-ASN : angle 4.47738 / 2.35 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8724 (mpp) cc_final: 0.7855 (ptp) REVERT: A 157 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7294 (mm-40) REVERT: A 246 TRP cc_start: 0.8238 (m-10) cc_final: 0.7956 (m-10) REVERT: A 415 LYS cc_start: 0.8197 (tppp) cc_final: 0.7809 (ttpt) REVERT: B 96 MET cc_start: 0.7783 (ppp) cc_final: 0.7397 (ppp) REVERT: B 140 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8668 (p) REVERT: B 246 TRP cc_start: 0.8327 (m-10) cc_final: 0.7816 (m-10) REVERT: C 64 ASP cc_start: 0.8212 (p0) cc_final: 0.7941 (p0) REVERT: C 250 TRP cc_start: 0.8109 (m100) cc_final: 0.7820 (m100) REVERT: C 308 TYR cc_start: 0.8302 (t80) cc_final: 0.7724 (t80) REVERT: D 259 ARG cc_start: 0.7182 (mtp180) cc_final: 0.6977 (mtp180) REVERT: D 307 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8676 (tm-30) REVERT: E 174 ARG cc_start: 0.7550 (mtp-110) cc_final: 0.7044 (mtp85) REVERT: E 278 PRO cc_start: 0.8959 (Cg_exo) cc_final: 0.8670 (Cg_endo) outliers start: 50 outliers final: 38 residues processed: 232 average time/residue: 0.0927 time to fit residues: 33.1361 Evaluate side-chains 214 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 312 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126774 restraints weight = 18875.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129620 restraints weight = 10982.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131545 restraints weight = 7500.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132761 restraints weight = 5728.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133626 restraints weight = 4763.594| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13862 Z= 0.178 Angle : 0.663 15.177 18878 Z= 0.323 Chirality : 0.047 0.624 2183 Planarity : 0.004 0.039 2335 Dihedral : 5.145 72.908 1816 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.71 % Allowed : 16.49 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.21), residues: 1666 helix: 1.33 (0.21), residues: 570 sheet: -1.85 (0.24), residues: 421 loop : -1.79 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 36 TYR 0.021 0.002 TYR E 325 PHE 0.020 0.002 PHE D 313 TRP 0.009 0.001 TRP B 177 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (13845) covalent geometry : angle 0.63737 / 0.32 (18835) SS BOND : bond 0.00557 / 0.28 ( 8) SS BOND : angle 2.19975 / 0.78 ( 16) hydrogen bonds : bond 0.03762 / 2.46 ( 670) hydrogen bonds : angle 4.64241 / 3.16 ( 2256) link_NAG-ASN : bond 0.00635 / 0.38 ( 9) link_NAG-ASN : angle 4.61448 / 2.58 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.6825 (p0) cc_final: 0.6569 (p0) REVERT: A 117 ASP cc_start: 0.7249 (p0) cc_final: 0.6966 (p0) REVERT: A 154 MET cc_start: 0.8722 (mpp) cc_final: 0.7905 (ptp) REVERT: A 157 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7272 (mm-40) REVERT: B 140 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 246 TRP cc_start: 0.8239 (m-10) cc_final: 0.7766 (m-10) REVERT: C 57 SER cc_start: 0.9010 (m) cc_final: 0.8436 (t) REVERT: C 64 ASP cc_start: 0.8198 (p0) cc_final: 0.7925 (p0) REVERT: C 250 TRP cc_start: 0.8159 (m100) cc_final: 0.7860 (m100) REVERT: C 308 TYR cc_start: 0.8310 (t80) cc_final: 0.7783 (t80) REVERT: C 404 LEU cc_start: 0.8561 (tt) cc_final: 0.8294 (tt) REVERT: D 226 GLN cc_start: 0.7933 (mt0) cc_final: 0.7447 (mm110) REVERT: D 250 TRP cc_start: 0.7671 (m100) cc_final: 0.7101 (m100) REVERT: E 174 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.6913 (mtp85) REVERT: E 237 ILE cc_start: 0.8954 (mt) cc_final: 0.8745 (mt) REVERT: E 278 PRO cc_start: 0.8928 (Cg_exo) cc_final: 0.8650 (Cg_endo) outliers start: 54 outliers final: 45 residues processed: 221 average time/residue: 0.0929 time to fit residues: 31.7125 Evaluate side-chains 218 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 312 ASN C 273 GLN ** D 49 ASN ** 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 = 0.3616 r_free = 0.3616 target = 0.143610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126528 restraints weight = 18914.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129472 restraints weight = 10916.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131369 restraints weight = 7383.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132641 restraints weight = 5631.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133483 restraints weight = 4647.296| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13862 Z= 0.158 Angle : 0.639 17.530 18878 Z= 0.311 Chirality : 0.046 0.699 2183 Planarity : 0.004 0.036 2335 Dihedral : 5.038 70.477 1816 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.05 % Allowed : 18.08 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1666 helix: 1.46 (0.21), residues: 570 sheet: -1.73 (0.24), residues: 421 loop : -1.72 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 259 TYR 0.019 0.001 TYR C 135 PHE 0.022 0.002 PHE D 313 TRP 0.034 0.001 TRP A 246 HIS 0.002 0.000 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (13845) covalent geometry : angle 0.60888 / 0.30 (18835) SS BOND : bond 0.00282 / 0.16 ( 8) SS BOND : angle 2.10771 / 0.72 ( 16) hydrogen bonds : bond 0.03648 / 2.38 ( 670) hydrogen bonds : angle 4.50208 / 3.07 ( 2256) link_NAG-ASN : bond 0.00786 / 0.45 ( 9) link_NAG-ASN : angle 4.94530 / 2.78 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.6875 (p0) cc_final: 0.6495 (p0) REVERT: A 154 MET cc_start: 0.8709 (mpp) cc_final: 0.7931 (ptp) REVERT: A 157 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7239 (mm-40) REVERT: B 140 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8726 (p) REVERT: B 246 TRP cc_start: 0.8144 (m-10) cc_final: 0.7719 (m-10) REVERT: C 57 SER cc_start: 0.9022 (m) cc_final: 0.8496 (t) REVERT: C 250 TRP cc_start: 0.8178 (m100) cc_final: 0.7879 (m100) REVERT: C 404 LEU cc_start: 0.8563 (tt) cc_final: 0.8284 (tt) REVERT: D 226 GLN cc_start: 0.7954 (mt0) cc_final: 0.7588 (mm110) REVERT: D 250 TRP cc_start: 0.7644 (m100) cc_final: 0.7093 (m100) REVERT: D 277 SER cc_start: 0.8116 (m) cc_final: 0.7851 (p) REVERT: E 112 MET cc_start: 0.7435 (mtp) cc_final: 0.7194 (mtt) REVERT: E 116 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8375 (pp) REVERT: E 174 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.7028 (mtp85) REVERT: E 278 PRO cc_start: 0.8946 (Cg_exo) cc_final: 0.8712 (Cg_endo) outliers start: 59 outliers final: 45 residues processed: 226 average time/residue: 0.0967 time to fit residues: 33.9571 Evaluate side-chains 223 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 72 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130744 restraints weight = 18643.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133704 restraints weight = 10800.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135629 restraints weight = 7316.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136651 restraints weight = 5564.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137647 restraints weight = 4701.232| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13862 Z= 0.119 Angle : 0.649 19.648 18878 Z= 0.307 Chirality : 0.043 0.236 2183 Planarity : 0.004 0.047 2335 Dihedral : 4.808 65.529 1816 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.51 % Allowed : 19.04 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.21), residues: 1666 helix: 1.58 (0.22), residues: 574 sheet: -1.50 (0.24), residues: 434 loop : -1.57 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 66 TYR 0.020 0.001 TYR C 135 PHE 0.023 0.001 PHE D 313 TRP 0.046 0.001 TRP A 246 HIS 0.002 0.000 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (13845) covalent geometry : angle 0.59831 / 0.29 (18835) SS BOND : bond 0.00257 / 0.14 ( 8) SS BOND : angle 1.85919 / 0.63 ( 16) hydrogen bonds : bond 0.03455 / 2.26 ( 670) hydrogen bonds : angle 4.34565 / 2.97 ( 2256) link_NAG-ASN : bond 0.01155 / 0.61 ( 9) link_NAG-ASN : angle 6.56677 / 4.66 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8661 (mpp) cc_final: 0.7847 (ptp) REVERT: B 140 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8622 (p) REVERT: B 147 MET cc_start: 0.8333 (mtt) cc_final: 0.8098 (mtt) REVERT: C 57 SER cc_start: 0.9047 (m) cc_final: 0.8545 (t) REVERT: C 73 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: C 154 MET cc_start: 0.7469 (mtm) cc_final: 0.7202 (mpp) REVERT: C 250 TRP cc_start: 0.8208 (m100) cc_final: 0.7852 (m100) REVERT: C 404 LEU cc_start: 0.8561 (tt) cc_final: 0.8298 (tt) REVERT: D 226 GLN cc_start: 0.7876 (mt0) cc_final: 0.7579 (mm110) REVERT: D 250 TRP cc_start: 0.7618 (m100) cc_final: 0.7016 (m100) REVERT: D 302 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: E 29 VAL cc_start: 0.5684 (OUTLIER) cc_final: 0.5456 (m) REVERT: E 174 ARG cc_start: 0.7470 (mtp-110) cc_final: 0.7176 (mtp85) REVERT: E 278 PRO cc_start: 0.8910 (Cg_exo) cc_final: 0.8670 (Cg_endo) outliers start: 51 outliers final: 35 residues processed: 223 average time/residue: 0.1005 time to fit residues: 35.1069 Evaluate side-chains 207 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 177 TRP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN E 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123568 restraints weight = 18874.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126460 restraints weight = 11001.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128371 restraints weight = 7508.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129640 restraints weight = 5728.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130323 restraints weight = 4748.603| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13862 Z= 0.210 Angle : 0.694 13.346 18878 Z= 0.336 Chirality : 0.046 0.303 2183 Planarity : 0.004 0.051 2335 Dihedral : 5.061 64.160 1816 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.26 % Allowed : 19.45 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.21), residues: 1666 helix: 1.47 (0.21), residues: 570 sheet: -1.54 (0.24), residues: 434 loop : -1.62 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 259 TYR 0.028 0.002 TYR B 308 PHE 0.023 0.002 PHE D 313 TRP 0.064 0.002 TRP A 246 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (13845) covalent geometry : angle 0.67028 / 0.33 (18835) SS BOND : bond 0.00289 / 0.18 ( 8) SS BOND : angle 1.97376 / 0.71 ( 16) hydrogen bonds : bond 0.03854 / 2.52 ( 670) hydrogen bonds : angle 4.52744 / 3.09 ( 2256) link_NAG-ASN : bond 0.00536 / 0.34 ( 9) link_NAG-ASN : angle 4.57051 / 2.50 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8741 (mpp) cc_final: 0.7981 (ptp) REVERT: B 140 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8675 (p) REVERT: B 246 TRP cc_start: 0.8169 (m-10) cc_final: 0.7813 (m-10) REVERT: C 57 SER cc_start: 0.9093 (m) cc_final: 0.8596 (t) REVERT: C 233 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7516 (tm-30) REVERT: C 250 TRP cc_start: 0.8326 (m100) cc_final: 0.7948 (m100) REVERT: C 312 ASN cc_start: 0.7837 (OUTLIER) cc_final: 0.7489 (t0) REVERT: D 226 GLN cc_start: 0.7988 (mt0) cc_final: 0.7635 (mm110) REVERT: D 250 TRP cc_start: 0.7620 (m100) cc_final: 0.7044 (m100) REVERT: D 259 ARG cc_start: 0.7152 (mtp180) cc_final: 0.6255 (mtp-110) REVERT: E 174 ARG cc_start: 0.7575 (mtp-110) cc_final: 0.7322 (mtp85) REVERT: E 278 PRO cc_start: 0.8868 (Cg_exo) cc_final: 0.8612 (Cg_endo) outliers start: 62 outliers final: 48 residues processed: 233 average time/residue: 0.0924 time to fit residues: 33.5863 Evaluate side-chains 233 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 177 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 29 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 117 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125834 restraints weight = 18542.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128721 restraints weight = 10859.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130612 restraints weight = 7458.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131865 restraints weight = 5717.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132529 restraints weight = 4752.911| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13862 Z= 0.149 Angle : 0.636 8.901 18878 Z= 0.311 Chirality : 0.045 0.256 2183 Planarity : 0.004 0.046 2335 Dihedral : 4.966 66.926 1816 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.71 % Allowed : 20.34 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1666 helix: 1.52 (0.21), residues: 570 sheet: -1.46 (0.24), residues: 434 loop : -1.49 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 259 TYR 0.027 0.001 TYR E 113 PHE 0.025 0.001 PHE D 313 TRP 0.075 0.002 TRP A 246 HIS 0.001 0.000 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (13845) covalent geometry : angle 0.62249 / 0.31 (18835) SS BOND : bond 0.00254 / 0.15 ( 8) SS BOND : angle 1.82405 / 0.63 ( 16) hydrogen bonds : bond 0.03610 / 2.36 ( 670) hydrogen bonds : angle 4.42741 / 3.02 ( 2256) link_NAG-ASN : bond 0.00411 / 0.29 ( 9) link_NAG-ASN : angle 3.27766 / 1.74 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8701 (mpp) cc_final: 0.7893 (ptp) REVERT: A 206 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.8916 (t) REVERT: B 140 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8588 (p) REVERT: C 57 SER cc_start: 0.9070 (m) cc_final: 0.8654 (t) REVERT: C 73 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8247 (pt0) REVERT: C 180 ASP cc_start: 0.6844 (p0) cc_final: 0.6616 (p0) REVERT: C 233 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7862 (tm-30) REVERT: C 250 TRP cc_start: 0.8258 (m100) cc_final: 0.7928 (m100) REVERT: C 404 LEU cc_start: 0.8624 (tt) cc_final: 0.8335 (tt) REVERT: D 226 GLN cc_start: 0.7966 (mt0) cc_final: 0.7601 (mm110) REVERT: D 250 TRP cc_start: 0.7580 (m100) cc_final: 0.7038 (m100) REVERT: D 302 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: E 174 ARG cc_start: 0.7552 (mtp-110) cc_final: 0.7321 (mtp85) REVERT: E 278 PRO cc_start: 0.8850 (Cg_exo) cc_final: 0.8627 (Cg_endo) outliers start: 54 outliers final: 43 residues processed: 221 average time/residue: 0.0920 time to fit residues: 31.8011 Evaluate side-chains 223 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 177 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124243 restraints weight = 18978.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127111 restraints weight = 11005.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129052 restraints weight = 7480.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130177 restraints weight = 5698.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131106 restraints weight = 4778.843| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13862 Z= 0.182 Angle : 0.701 19.442 18878 Z= 0.333 Chirality : 0.045 0.216 2183 Planarity : 0.004 0.053 2335 Dihedral : 5.108 74.429 1816 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.78 % Allowed : 20.69 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.21), residues: 1666 helix: 1.48 (0.21), residues: 566 sheet: -1.36 (0.24), residues: 418 loop : -1.49 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 259 TYR 0.030 0.002 TYR E 113 PHE 0.026 0.002 PHE D 313 TRP 0.080 0.002 TRP A 246 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (13845) covalent geometry : angle 0.67275 / 0.33 (18835) SS BOND : bond 0.00264 / 0.16 ( 8) SS BOND : angle 1.81125 / 0.64 ( 16) hydrogen bonds : bond 0.03747 / 2.45 ( 670) hydrogen bonds : angle 4.50342 / 3.07 ( 2256) link_NAG-ASN : bond 0.00701 / 0.41 ( 9) link_NAG-ASN : angle 5.05180 / 3.25 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8711 (mpp) cc_final: 0.7919 (ptp) REVERT: A 206 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.8952 (t) REVERT: B 140 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8637 (p) REVERT: C 57 SER cc_start: 0.9112 (m) cc_final: 0.8674 (t) REVERT: C 73 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8324 (pt0) REVERT: C 180 ASP cc_start: 0.6945 (p0) cc_final: 0.6675 (p0) REVERT: C 233 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7936 (tm-30) REVERT: C 250 TRP cc_start: 0.8265 (m100) cc_final: 0.7957 (m100) REVERT: C 404 LEU cc_start: 0.8657 (tt) cc_final: 0.8370 (tt) REVERT: D 226 GLN cc_start: 0.8014 (mt0) cc_final: 0.7639 (mm110) REVERT: D 250 TRP cc_start: 0.7582 (m100) cc_final: 0.7033 (m100) REVERT: D 259 ARG cc_start: 0.6896 (mtp85) cc_final: 0.6585 (mtp-110) REVERT: D 302 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: E 126 GLU cc_start: 0.7707 (tt0) cc_final: 0.7493 (tt0) REVERT: E 174 ARG cc_start: 0.7569 (mtp-110) cc_final: 0.7337 (mtp85) REVERT: E 278 PRO cc_start: 0.8824 (Cg_exo) cc_final: 0.8597 (Cg_endo) outliers start: 55 outliers final: 47 residues processed: 226 average time/residue: 0.0932 time to fit residues: 32.9173 Evaluate side-chains 234 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 177 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127088 restraints weight = 18645.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130034 restraints weight = 10724.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131949 restraints weight = 7232.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133183 restraints weight = 5490.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133710 restraints weight = 4539.250| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13862 Z= 0.132 Angle : 0.641 9.388 18878 Z= 0.310 Chirality : 0.045 0.379 2183 Planarity : 0.004 0.051 2335 Dihedral : 4.886 65.250 1816 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.44 % Allowed : 20.89 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.54 (0.21), residues: 1666 helix: 1.61 (0.21), residues: 566 sheet: -1.36 (0.25), residues: 414 loop : -1.34 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 259 TYR 0.022 0.001 TYR E 113 PHE 0.026 0.001 PHE D 313 TRP 0.056 0.001 TRP A 246 HIS 0.002 0.000 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (13845) covalent geometry : angle 0.62907 / 0.31 (18835) SS BOND : bond 0.00251 / 0.14 ( 8) SS BOND : angle 1.70980 / 0.58 ( 16) hydrogen bonds : bond 0.03517 / 2.30 ( 670) hydrogen bonds : angle 4.40193 / 3.01 ( 2256) link_NAG-ASN : bond 0.00673 / 0.39 ( 9) link_NAG-ASN : angle 3.04438 / 1.70 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7137 (p0) cc_final: 0.6743 (p0) REVERT: A 154 MET cc_start: 0.8676 (mpp) cc_final: 0.7897 (ptp) REVERT: A 206 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8927 (t) REVERT: B 25 MET cc_start: 0.8311 (ptm) cc_final: 0.7391 (ppp) REVERT: B 140 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8536 (p) REVERT: C 57 SER cc_start: 0.9104 (m) cc_final: 0.8694 (t) REVERT: C 73 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: C 180 ASP cc_start: 0.6857 (p0) cc_final: 0.6631 (p0) REVERT: C 233 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7882 (tm-30) REVERT: C 404 LEU cc_start: 0.8654 (tt) cc_final: 0.8374 (tt) REVERT: D 226 GLN cc_start: 0.7962 (mt0) cc_final: 0.7644 (mm110) REVERT: D 250 TRP cc_start: 0.7476 (m100) cc_final: 0.6935 (m100) REVERT: D 259 ARG cc_start: 0.6833 (mtp85) cc_final: 0.6227 (mtp-110) REVERT: D 302 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: E 126 GLU cc_start: 0.7652 (tt0) cc_final: 0.7437 (tt0) REVERT: E 174 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.7316 (mtp85) outliers start: 50 outliers final: 46 residues processed: 234 average time/residue: 0.0922 time to fit residues: 33.6898 Evaluate side-chains 233 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 177 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126778 restraints weight = 18700.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129657 restraints weight = 10737.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131567 restraints weight = 7224.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132696 restraints weight = 5474.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133553 restraints weight = 4563.507| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 13862 Z= 0.189 Angle : 0.861 59.192 18878 Z= 0.471 Chirality : 0.053 1.314 2183 Planarity : 0.004 0.050 2335 Dihedral : 4.916 65.247 1816 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.71 % Allowed : 21.58 % Favored : 74.71 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.21), residues: 1666 helix: 1.57 (0.21), residues: 566 sheet: -1.35 (0.25), residues: 414 loop : -1.34 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 259 TYR 0.021 0.001 TYR E 113 PHE 0.025 0.001 PHE D 313 TRP 0.049 0.001 TRP A 246 HIS 0.001 0.000 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (13845) covalent geometry : angle 0.85284 / 0.47 (18835) SS BOND : bond 0.00254 / 0.14 ( 8) SS BOND : angle 1.68199 / 0.58 ( 16) hydrogen bonds : bond 0.03554 / 2.34 ( 670) hydrogen bonds : angle 4.40426 / 3.01 ( 2256) link_NAG-ASN : bond 0.00646 / 0.38 ( 9) link_NAG-ASN : angle 3.03946 / 1.70 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1897.93 seconds wall clock time: 33 minutes 45.55 seconds (2025.55 seconds total)