Starting phenix.real_space_refine on Wed Mar 4 11:47:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5bkg_9404/03_2026/5bkg_9404.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkg_9404/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/5bkg_9404/03_2026/5bkg_9404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkg_9404/03_2026/5bkg_9404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5bkg_9404/03_2026/5bkg_9404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkg_9404/03_2026/5bkg_9404.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.45, per 1000 atoms: 0.26 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: 1.01 Conformation dependent library (CDL) restraints added in 780.5 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: 0.44 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: 2.43 Time building geometry restraints manager: 1.43 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 - 24.14: 7951 24.14 - 48.28: 335 48.28 - 72.43: 17 72.43 - 96.57: 11 96.57 - 120.71: 2 Dihedral angle restraints: 8316 sinusoidal: 3331 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 8313 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: 1.200 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.280 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 : 12.911 120.708 5058 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 covalent geometry : bond 0.00436 (13845) covalent geometry : angle 0.57943 (18835) SS BOND : bond 0.00369 ( 8) SS BOND : angle 2.10199 ( 16) hydrogen bonds : bond 0.10864 ( 670) hydrogen bonds : angle 6.64399 ( 2256) link_NAG-ASN : bond 0.00689 ( 9) link_NAG-ASN : angle 3.77092 ( 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 : 0.346 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: 0.0968 time to fit residues: 40.8090 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 : 0.356 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 68 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137775 restraints weight = 18450.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140640 restraints weight = 10903.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.142535 restraints weight = 7450.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143576 restraints weight = 5675.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144539 restraints weight = 4774.041| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13862 Z= 0.142 Angle : 0.672 12.848 18878 Z= 0.328 Chirality : 0.046 0.424 2183 Planarity : 0.004 0.048 2335 Dihedral : 6.493 80.424 2005 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.72 % Allowed : 12.16 % Favored : 86.12 % 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: -1.97 (0.20), residues: 1666 helix: 0.50 (0.21), residues: 602 sheet: -2.30 (0.26), residues: 350 loop : -2.35 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 66 TYR 0.019 0.001 TYR C 308 PHE 0.017 0.002 PHE D 313 TRP 0.008 0.001 TRP E 267 HIS 0.007 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00317 (13845) covalent geometry : angle 0.64154 (18835) SS BOND : bond 0.00478 ( 8) SS BOND : angle 2.01945 ( 16) hydrogen bonds : bond 0.03864 ( 670) hydrogen bonds : angle 4.85769 ( 2256) link_NAG-ASN : bond 0.00801 ( 9) link_NAG-ASN : angle 5.07361 ( 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 238 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7076 (mm-40) REVERT: A 294 MET cc_start: 0.8081 (mmm) cc_final: 0.7878 (mmm) REVERT: A 415 LYS cc_start: 0.8046 (tppp) cc_final: 0.7781 (ttpt) REVERT: B 246 TRP cc_start: 0.8154 (m-10) cc_final: 0.7703 (m-10) REVERT: C 64 ASP cc_start: 0.8109 (p0) cc_final: 0.7898 (p0) REVERT: C 109 ASN cc_start: 0.8681 (p0) cc_final: 0.8341 (p0) REVERT: C 250 TRP cc_start: 0.7875 (m100) cc_final: 0.7634 (m100) REVERT: C 270 MET cc_start: 0.8645 (tpp) cc_final: 0.7553 (tpp) REVERT: C 308 TYR cc_start: 0.8246 (t80) cc_final: 0.7674 (t80) REVERT: D 68 ASN cc_start: 0.8227 (p0) cc_final: 0.8000 (p0) REVERT: D 259 ARG cc_start: 0.7037 (mtp180) cc_final: 0.6745 (mtp180) REVERT: E 174 ARG cc_start: 0.7388 (mtp-110) cc_final: 0.7057 (mtp85) REVERT: E 237 ILE cc_start: 0.8892 (mt) cc_final: 0.8624 (mt) outliers start: 25 outliers final: 17 residues processed: 227 average time/residue: 0.1030 time to fit residues: 35.0493 Evaluate side-chains 193 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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: 8.9990 chunk 45 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 0.0070 chunk 100 optimal weight: 0.0070 chunk 116 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 overall best weight: 1.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN C 68 ASN C 208 HIS C 273 GLN ** 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 = 0.3694 r_free = 0.3694 target = 0.149855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133399 restraints weight = 18609.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136360 restraints weight = 10697.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138256 restraints weight = 7189.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139550 restraints weight = 5458.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.140291 restraints weight = 4492.788| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13862 Z= 0.139 Angle : 0.614 11.807 18878 Z= 0.302 Chirality : 0.044 0.488 2183 Planarity : 0.004 0.041 2335 Dihedral : 5.997 73.909 2005 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.96 % Allowed : 14.43 % Favored : 82.61 % 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: -1.15 (0.21), residues: 1666 helix: 1.32 (0.21), residues: 574 sheet: -1.86 (0.27), residues: 355 loop : -1.89 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 36 TYR 0.019 0.001 TYR E 325 PHE 0.018 0.001 PHE C 115 TRP 0.008 0.001 TRP E 267 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00318 (13845) covalent geometry : angle 0.59114 (18835) SS BOND : bond 0.00360 ( 8) SS BOND : angle 1.83597 ( 16) hydrogen bonds : bond 0.03625 ( 670) hydrogen bonds : angle 4.56296 ( 2256) link_NAG-ASN : bond 0.00579 ( 9) link_NAG-ASN : angle 4.20018 ( 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 239 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8687 (mpp) cc_final: 0.7775 (ptp) REVERT: A 157 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7209 (mm-40) REVERT: A 246 TRP cc_start: 0.8112 (m-10) cc_final: 0.7818 (m-10) REVERT: A 415 LYS cc_start: 0.8085 (tppp) cc_final: 0.7645 (ttpt) REVERT: B 140 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8690 (p) REVERT: C 64 ASP cc_start: 0.8130 (p0) cc_final: 0.7910 (p0) REVERT: C 250 TRP cc_start: 0.8026 (m100) cc_final: 0.7719 (m100) REVERT: C 308 TYR cc_start: 0.8164 (t80) cc_final: 0.7673 (t80) REVERT: D 302 PHE cc_start: 0.7690 (m-80) cc_final: 0.7288 (m-80) REVERT: E 174 ARG cc_start: 0.7437 (mtp-110) cc_final: 0.6980 (mtp85) REVERT: E 278 PRO cc_start: 0.8933 (Cg_exo) cc_final: 0.8656 (Cg_endo) outliers start: 43 outliers final: 30 residues processed: 224 average time/residue: 0.1017 time to fit residues: 34.2273 Evaluate side-chains 200 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 114 ASN 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 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 89 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 96 MET 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 E residue 167 LEU Chi-restraints excluded: chain E residue 195 SER 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: 4.9990 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 152 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS B 312 ASN ** 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 = 0.3622 r_free = 0.3622 target = 0.143877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127020 restraints weight = 18787.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129865 restraints weight = 10858.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131775 restraints weight = 7362.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132983 restraints weight = 5604.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133650 restraints weight = 4660.971| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13862 Z= 0.192 Angle : 0.663 12.456 18878 Z= 0.325 Chirality : 0.046 0.443 2183 Planarity : 0.004 0.040 2335 Dihedral : 5.858 70.139 2005 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.57 % Allowed : 16.22 % Favored : 80.21 % 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: -1.04 (0.21), residues: 1666 helix: 1.39 (0.21), residues: 570 sheet: -1.80 (0.24), residues: 434 loop : -1.71 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 259 TYR 0.025 0.002 TYR E 325 PHE 0.018 0.002 PHE D 313 TRP 0.008 0.001 TRP B 177 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00452 (13845) covalent geometry : angle 0.64009 (18835) SS BOND : bond 0.00506 ( 8) SS BOND : angle 2.17529 ( 16) hydrogen bonds : bond 0.03795 ( 670) hydrogen bonds : angle 4.59416 ( 2256) link_NAG-ASN : bond 0.00587 ( 9) link_NAG-ASN : angle 4.37578 ( 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 249 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.6762 (p0) cc_final: 0.6506 (p0) REVERT: A 117 ASP cc_start: 0.7155 (p0) cc_final: 0.6919 (p0) REVERT: A 154 MET cc_start: 0.8680 (mpp) cc_final: 0.7863 (ptp) REVERT: A 157 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7295 (mm-40) REVERT: A 246 TRP cc_start: 0.8210 (m-10) cc_final: 0.7900 (m-10) REVERT: B 126 ARG cc_start: 0.8627 (ttm110) cc_final: 0.8020 (mtp-110) REVERT: B 140 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8746 (p) REVERT: B 246 TRP cc_start: 0.8198 (m-10) cc_final: 0.7718 (m-10) REVERT: C 64 ASP cc_start: 0.8164 (p0) cc_final: 0.7914 (p0) REVERT: C 250 TRP cc_start: 0.8188 (m100) cc_final: 0.7879 (m100) REVERT: C 308 TYR cc_start: 0.8206 (t80) cc_final: 0.7636 (t80) REVERT: C 404 LEU cc_start: 0.8618 (tt) cc_final: 0.8338 (tt) REVERT: D 226 GLN cc_start: 0.7956 (mt0) cc_final: 0.7470 (mm110) REVERT: D 250 TRP cc_start: 0.7557 (m100) cc_final: 0.7014 (m100) REVERT: D 307 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8710 (tm-30) REVERT: E 174 ARG cc_start: 0.7462 (mtp-110) cc_final: 0.6954 (mtp85) REVERT: E 278 PRO cc_start: 0.8891 (Cg_exo) cc_final: 0.8632 (Cg_endo) outliers start: 52 outliers final: 41 residues processed: 231 average time/residue: 0.0933 time to fit residues: 33.3594 Evaluate side-chains 220 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 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 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 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 96 MET Chi-restraints excluded: chain D residue 118 VAL 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 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 232 THR Chi-restraints excluded: chain E residue 264 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 0.0970 chunk 16 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3667 r_free = 0.3667 target = 0.147862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130929 restraints weight = 18734.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133876 restraints weight = 10845.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135807 restraints weight = 7341.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.137047 restraints weight = 5591.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137718 restraints weight = 4627.706| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13862 Z= 0.119 Angle : 0.603 11.182 18878 Z= 0.296 Chirality : 0.044 0.436 2183 Planarity : 0.004 0.037 2335 Dihedral : 5.447 67.022 2005 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.23 % Allowed : 17.66 % Favored : 79.11 % 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: -0.77 (0.21), residues: 1666 helix: 1.54 (0.21), residues: 574 sheet: -1.59 (0.24), residues: 434 loop : -1.54 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 259 TYR 0.021 0.001 TYR E 325 PHE 0.020 0.001 PHE D 313 TRP 0.010 0.001 TRP C 411 HIS 0.002 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00264 (13845) covalent geometry : angle 0.58265 (18835) SS BOND : bond 0.00282 ( 8) SS BOND : angle 2.08195 ( 16) hydrogen bonds : bond 0.03482 ( 670) hydrogen bonds : angle 4.38471 ( 2256) link_NAG-ASN : bond 0.00597 ( 9) link_NAG-ASN : angle 3.87833 ( 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 237 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8675 (mpp) cc_final: 0.7836 (ptp) REVERT: A 157 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7244 (mm-40) REVERT: B 140 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8645 (p) REVERT: C 64 ASP cc_start: 0.8137 (p0) cc_final: 0.7889 (p0) REVERT: C 73 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: C 250 TRP cc_start: 0.8167 (m100) cc_final: 0.7840 (m100) REVERT: C 308 TYR cc_start: 0.8110 (t80) cc_final: 0.7599 (t80) REVERT: C 404 LEU cc_start: 0.8527 (tt) cc_final: 0.8268 (tt) REVERT: D 250 TRP cc_start: 0.7540 (m100) cc_final: 0.6996 (m100) REVERT: D 277 SER cc_start: 0.8228 (m) cc_final: 0.7965 (t) REVERT: D 302 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: E 116 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8374 (pp) REVERT: E 174 ARG cc_start: 0.7406 (mtp-110) cc_final: 0.7009 (mtp85) REVERT: E 278 PRO cc_start: 0.8949 (Cg_exo) cc_final: 0.8713 (Cg_endo) outliers start: 47 outliers final: 33 residues processed: 218 average time/residue: 0.0920 time to fit residues: 31.0830 Evaluate side-chains 211 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU 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 62 THR Chi-restraints excluded: chain B residue 76 ASN 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 183 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 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 54 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 72 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3646 r_free = 0.3646 target = 0.146062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129067 restraints weight = 18695.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131957 restraints weight = 10843.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133850 restraints weight = 7390.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.134873 restraints weight = 5662.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.135835 restraints weight = 4786.614| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13862 Z= 0.146 Angle : 0.617 10.708 18878 Z= 0.301 Chirality : 0.044 0.422 2183 Planarity : 0.004 0.036 2335 Dihedral : 5.259 64.243 2005 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.92 % Allowed : 18.08 % Favored : 78.01 % 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: -0.70 (0.21), residues: 1666 helix: 1.64 (0.21), residues: 570 sheet: -1.49 (0.24), residues: 434 loop : -1.56 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 259 TYR 0.020 0.001 TYR C 135 PHE 0.026 0.001 PHE A 406 TRP 0.037 0.001 TRP A 246 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00342 (13845) covalent geometry : angle 0.59912 (18835) SS BOND : bond 0.00267 ( 8) SS BOND : angle 1.95725 ( 16) hydrogen bonds : bond 0.03532 ( 670) hydrogen bonds : angle 4.35106 ( 2256) link_NAG-ASN : bond 0.00528 ( 9) link_NAG-ASN : angle 3.72440 ( 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 235 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8646 (mpp) cc_final: 0.7816 (ptp) REVERT: B 140 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8685 (p) REVERT: C 64 ASP cc_start: 0.8159 (p0) cc_final: 0.7938 (p0) REVERT: C 73 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: C 154 MET cc_start: 0.7791 (mpp) cc_final: 0.7514 (ptp) REVERT: C 250 TRP cc_start: 0.8229 (m100) cc_final: 0.7885 (m100) REVERT: C 308 TYR cc_start: 0.8138 (t80) cc_final: 0.7599 (t80) REVERT: C 404 LEU cc_start: 0.8622 (tt) cc_final: 0.8331 (tt) REVERT: D 170 MET cc_start: 0.9029 (tpp) cc_final: 0.8778 (mmt) REVERT: D 226 GLN cc_start: 0.7761 (mt0) cc_final: 0.7538 (mm110) REVERT: D 250 TRP cc_start: 0.7581 (m100) cc_final: 0.7015 (m100) REVERT: D 259 ARG cc_start: 0.6802 (mtp180) cc_final: 0.6088 (mtp-110) REVERT: D 302 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: E 116 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8400 (pp) REVERT: E 174 ARG cc_start: 0.7436 (mtp-110) cc_final: 0.7140 (mtp85) REVERT: E 278 PRO cc_start: 0.8894 (Cg_exo) cc_final: 0.8650 (Cg_endo) outliers start: 57 outliers final: 43 residues processed: 213 average time/residue: 0.0923 time to fit residues: 30.7024 Evaluate side-chains 219 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 292 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 76 ASN 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 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 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 54 SER 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 189 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 231 LEU 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 116 LEU Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 3.9990 chunk 140 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.0470 chunk 109 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 50 optimal weight: 0.0470 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134452 restraints weight = 18664.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.137452 restraints weight = 10778.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139431 restraints weight = 7304.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140545 restraints weight = 5553.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141512 restraints weight = 4657.377| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 13862 Z= 0.107 Angle : 0.583 9.311 18878 Z= 0.287 Chirality : 0.043 0.380 2183 Planarity : 0.004 0.035 2335 Dihedral : 4.789 55.658 2005 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.23 % Allowed : 19.18 % Favored : 77.59 % 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: -0.41 (0.21), residues: 1666 helix: 1.75 (0.22), residues: 578 sheet: -1.22 (0.25), residues: 425 loop : -1.41 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 259 TYR 0.027 0.001 TYR B 308 PHE 0.023 0.001 PHE D 313 TRP 0.048 0.001 TRP A 246 HIS 0.001 0.000 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00233 (13845) covalent geometry : angle 0.57016 (18835) SS BOND : bond 0.00264 ( 8) SS BOND : angle 1.74235 ( 16) hydrogen bonds : bond 0.03299 ( 670) hydrogen bonds : angle 4.21335 ( 2256) link_NAG-ASN : bond 0.00566 ( 9) link_NAG-ASN : angle 3.05357 ( 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 245 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8575 (mpp) cc_final: 0.7689 (ptp) REVERT: B 140 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8512 (p) REVERT: C 64 ASP cc_start: 0.8118 (p0) cc_final: 0.7907 (p0) REVERT: C 73 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8130 (pt0) REVERT: C 180 ASP cc_start: 0.6728 (p0) cc_final: 0.6494 (p0) REVERT: C 250 TRP cc_start: 0.8166 (m100) cc_final: 0.7806 (m100) REVERT: C 404 LEU cc_start: 0.8527 (tt) cc_final: 0.8251 (tt) REVERT: D 226 GLN cc_start: 0.7759 (mt0) cc_final: 0.7511 (mm110) REVERT: D 250 TRP cc_start: 0.7493 (m100) cc_final: 0.6937 (m100) REVERT: E 174 ARG cc_start: 0.7332 (mtp-110) cc_final: 0.6999 (mtp85) outliers start: 47 outliers final: 32 residues processed: 224 average time/residue: 0.0867 time to fit residues: 30.4281 Evaluate side-chains 214 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU 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 76 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 271 THR 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 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 141 LEU 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 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 264 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: 9.9990 chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 0.1980 chunk 83 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.3698 r_free = 0.3698 target = 0.150417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133450 restraints weight = 18432.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.136367 restraints weight = 10709.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138300 restraints weight = 7306.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139580 restraints weight = 5570.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140260 restraints weight = 4614.284| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13862 Z= 0.114 Angle : 0.605 9.492 18878 Z= 0.295 Chirality : 0.043 0.381 2183 Planarity : 0.004 0.053 2335 Dihedral : 4.695 51.728 2005 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.75 % Allowed : 20.89 % Favored : 76.36 % 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: -0.28 (0.21), residues: 1666 helix: 1.85 (0.21), residues: 578 sheet: -1.10 (0.25), residues: 425 loop : -1.36 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 259 TYR 0.028 0.001 TYR A 308 PHE 0.025 0.001 PHE D 313 TRP 0.076 0.001 TRP A 246 HIS 0.002 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00256 (13845) covalent geometry : angle 0.59257 (18835) SS BOND : bond 0.00259 ( 8) SS BOND : angle 1.68570 ( 16) hydrogen bonds : bond 0.03252 ( 670) hydrogen bonds : angle 4.18362 ( 2256) link_NAG-ASN : bond 0.00533 ( 9) link_NAG-ASN : angle 3.01455 ( 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 223 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8542 (mpp) cc_final: 0.7643 (ptp) REVERT: B 140 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8529 (p) REVERT: C 73 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: C 180 ASP cc_start: 0.6724 (p0) cc_final: 0.6478 (p0) REVERT: C 250 TRP cc_start: 0.8154 (m100) cc_final: 0.7785 (m100) REVERT: C 270 MET cc_start: 0.8773 (tpp) cc_final: 0.7712 (tpp) REVERT: C 404 LEU cc_start: 0.8573 (tt) cc_final: 0.8326 (tt) REVERT: D 226 GLN cc_start: 0.7785 (mt0) cc_final: 0.7516 (mm110) REVERT: D 250 TRP cc_start: 0.7467 (m100) cc_final: 0.6918 (m100) REVERT: D 259 ARG cc_start: 0.6678 (mtp85) cc_final: 0.6061 (mtp-110) REVERT: E 174 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.6968 (mtp85) outliers start: 40 outliers final: 31 residues processed: 208 average time/residue: 0.0892 time to fit residues: 28.8695 Evaluate side-chains 206 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 110 GLU 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 399 PHE Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 MET 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 306 LEU 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 205 CYS Chi-restraints excluded: chain D residue 247 VAL 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 195 SER 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: 1.9990 chunk 14 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 73 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120228 restraints weight = 19190.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123018 restraints weight = 11137.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124827 restraints weight = 7630.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126077 restraints weight = 5888.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126756 restraints weight = 4907.622| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 13862 Z= 0.283 Angle : 0.763 10.423 18878 Z= 0.378 Chirality : 0.049 0.419 2183 Planarity : 0.005 0.049 2335 Dihedral : 5.465 61.284 2005 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.57 % Allowed : 20.41 % Favored : 76.01 % 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: -0.64 (0.21), residues: 1666 helix: 1.43 (0.21), residues: 570 sheet: -1.20 (0.25), residues: 395 loop : -1.48 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 259 TYR 0.049 0.002 TYR E 113 PHE 0.025 0.002 PHE C 70 TRP 0.091 0.002 TRP A 246 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00676 (13845) covalent geometry : angle 0.74767 (18835) SS BOND : bond 0.00361 ( 8) SS BOND : angle 2.08438 ( 16) hydrogen bonds : bond 0.04220 ( 670) hydrogen bonds : angle 4.68825 ( 2256) link_NAG-ASN : bond 0.00467 ( 9) link_NAG-ASN : angle 3.82981 ( 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 243 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8677 (mpp) cc_final: 0.7991 (ptp) REVERT: A 206 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9001 (t) REVERT: B 140 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8796 (p) REVERT: B 246 TRP cc_start: 0.8256 (m-10) cc_final: 0.7904 (m100) REVERT: C 73 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8462 (pt0) REVERT: C 233 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8072 (tm-30) REVERT: C 250 TRP cc_start: 0.8267 (m100) cc_final: 0.7934 (m100) REVERT: D 226 GLN cc_start: 0.7942 (mt0) cc_final: 0.7576 (mm110) REVERT: D 250 TRP cc_start: 0.7526 (m100) cc_final: 0.7036 (m100) REVERT: E 126 GLU cc_start: 0.8008 (tt0) cc_final: 0.7709 (tt0) outliers start: 52 outliers final: 40 residues processed: 224 average time/residue: 0.0892 time to fit residues: 31.0264 Evaluate side-chains 225 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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 399 PHE Chi-restraints excluded: chain B residue 76 ASN 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 219 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 MET 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 280 SER Chi-restraints excluded: chain C residue 299 LEU 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 148 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 177 TRP 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 391 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 195 SER 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: 3.9990 chunk 123 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN C 312 ASN ** 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 = 0.3628 r_free = 0.3628 target = 0.144689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127447 restraints weight = 18687.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130355 restraints weight = 10807.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132279 restraints weight = 7358.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133562 restraints weight = 5612.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134200 restraints weight = 4650.615| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13862 Z= 0.126 Angle : 0.638 9.590 18878 Z= 0.313 Chirality : 0.045 0.386 2183 Planarity : 0.004 0.048 2335 Dihedral : 5.057 58.234 2005 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.61 % Allowed : 21.31 % Favored : 76.08 % 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: -0.46 (0.21), residues: 1666 helix: 1.63 (0.21), residues: 570 sheet: -1.30 (0.25), residues: 414 loop : -1.28 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 259 TYR 0.028 0.001 TYR A 308 PHE 0.024 0.001 PHE D 313 TRP 0.075 0.002 TRP A 246 HIS 0.001 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00278 (13845) covalent geometry : angle 0.62440 (18835) SS BOND : bond 0.00271 ( 8) SS BOND : angle 1.78731 ( 16) hydrogen bonds : bond 0.03613 ( 670) hydrogen bonds : angle 4.43033 ( 2256) link_NAG-ASN : bond 0.00503 ( 9) link_NAG-ASN : angle 3.24670 ( 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 227 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7411 (pt0) REVERT: A 154 MET cc_start: 0.8666 (mpp) cc_final: 0.7863 (ptp) REVERT: A 206 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.8914 (t) REVERT: B 140 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8513 (p) REVERT: C 57 SER cc_start: 0.9057 (m) cc_final: 0.8589 (t) REVERT: C 73 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: C 180 ASP cc_start: 0.6927 (p0) cc_final: 0.6711 (p0) REVERT: C 250 TRP cc_start: 0.8230 (m100) cc_final: 0.7914 (m100) REVERT: C 404 LEU cc_start: 0.8648 (tt) cc_final: 0.8346 (tt) REVERT: D 226 GLN cc_start: 0.7876 (mt0) cc_final: 0.7545 (mm110) REVERT: D 250 TRP cc_start: 0.7477 (m100) cc_final: 0.6950 (m100) REVERT: D 259 ARG cc_start: 0.6728 (mtp85) cc_final: 0.6395 (mtp-110) outliers start: 38 outliers final: 26 residues processed: 211 average time/residue: 0.0902 time to fit residues: 29.6118 Evaluate side-chains 210 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 201 GLU 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 C residue 73 GLN 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 312 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 93 ASP 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 247 VAL Chi-restraints excluded: chain D residue 391 ILE 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 195 SER Chi-restraints excluded: chain E residue 264 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 21 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127180 restraints weight = 18808.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130119 restraints weight = 10871.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132013 restraints weight = 7380.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133262 restraints weight = 5657.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133979 restraints weight = 4705.018| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 13862 Z= 0.187 Angle : 0.867 59.190 18878 Z= 0.491 Chirality : 0.044 0.387 2183 Planarity : 0.004 0.047 2335 Dihedral : 5.055 58.242 2005 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.20 % Allowed : 22.13 % Favored : 75.67 % 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: -0.47 (0.21), residues: 1666 helix: 1.60 (0.21), residues: 570 sheet: -1.29 (0.25), residues: 414 loop : -1.28 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 259 TYR 0.069 0.002 TYR E 113 PHE 0.023 0.001 PHE D 313 TRP 0.066 0.002 TRP A 246 HIS 0.001 0.000 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00411 (13845) covalent geometry : angle 0.85732 (18835) SS BOND : bond 0.00268 ( 8) SS BOND : angle 1.76051 ( 16) hydrogen bonds : bond 0.03620 ( 670) hydrogen bonds : angle 4.43042 ( 2256) link_NAG-ASN : bond 0.00528 ( 9) link_NAG-ASN : angle 3.30891 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1800.97 seconds wall clock time: 32 minutes 3.53 seconds (1923.53 seconds total)