Starting phenix.real_space_refine on Thu Jul 31 10:07:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5bkg_9404/07_2025/5bkg_9404.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkg_9404/07_2025/5bkg_9404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5bkg_9404/07_2025/5bkg_9404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkg_9404/07_2025/5bkg_9404.map" model { file = "/net/cci-nas-00/data/ceres_data/5bkg_9404/07_2025/5bkg_9404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkg_9404/07_2025/5bkg_9404.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4, '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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4, '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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4, '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: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP: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: 8.73, per 1000 atoms: 0.65 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: 3.42 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.53 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: 4.35 Time building geometry restraints manager: 4.03 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 418 or resid 501 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 418 or resid 501 through 5 \ 02)) 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 418 or resid 501 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: 1.920 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 33.530 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.000 ------------------------------------------------------------------------------- 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 : 8.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP D 75 HIS 0.002 0.001 HIS C 208 PHE 0.021 0.001 PHE A 406 TYR 0.018 0.001 TYR B 308 ARG 0.004 0.000 ARG E 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 9) link_NAG-ASN : angle 3.77092 ( 27) hydrogen bonds : bond 0.10864 ( 670) hydrogen bonds : angle 6.64399 ( 2256) SS BOND : bond 0.00369 ( 8) SS BOND : angle 2.10199 ( 16) covalent geometry : bond 0.00436 (13845) covalent geometry : angle 0.57943 (18835) *********************** 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 : 1.546 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: 0.6901 (p0) cc_final: 0.6637 (p0) REVERT: E 125 ASN cc_start: 0.8420 (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: 0.2494 time to fit residues: 103.6116 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 : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 222 HIS B 312 ASN C 73 GLN C 184 GLN C 208 HIS C 312 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124803 restraints weight = 18832.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127510 restraints weight = 11152.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129364 restraints weight = 7717.661| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 13862 Z= 0.288 Angle : 0.790 15.284 18878 Z= 0.390 Chirality : 0.050 0.460 2183 Planarity : 0.005 0.050 2335 Dihedral : 7.027 83.985 2005 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.75 % Allowed : 13.47 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.20), residues: 1666 helix: 0.28 (0.20), residues: 598 sheet: -2.47 (0.24), residues: 379 loop : -2.54 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 177 HIS 0.006 0.001 HIS C 208 PHE 0.025 0.002 PHE B 152 TYR 0.016 0.002 TYR C 308 ARG 0.005 0.001 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 9) link_NAG-ASN : angle 5.45558 ( 27) hydrogen bonds : bond 0.04531 ( 670) hydrogen bonds : angle 5.15052 ( 2256) SS BOND : bond 0.00868 ( 8) SS BOND : angle 2.08849 ( 16) covalent geometry : bond 0.00684 (13845) covalent geometry : angle 0.76139 (18835) *********************** 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 250 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7226 (p0) cc_final: 0.6837 (p0) REVERT: A 157 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7424 (mm-40) REVERT: A 246 TRP cc_start: 0.8250 (m-10) cc_final: 0.8048 (m-10) REVERT: A 415 LYS cc_start: 0.8279 (tppp) cc_final: 0.7955 (ttpt) REVERT: B 109 ASN cc_start: 0.8522 (p0) cc_final: 0.7856 (p0) REVERT: B 246 TRP cc_start: 0.8394 (m-10) cc_final: 0.7848 (m-10) REVERT: C 57 SER cc_start: 0.8996 (m) cc_final: 0.8436 (t) REVERT: C 64 ASP cc_start: 0.8286 (p0) cc_final: 0.7974 (p0) REVERT: C 250 TRP cc_start: 0.8133 (m100) cc_final: 0.7737 (m100) REVERT: C 308 TYR cc_start: 0.8522 (t80) cc_final: 0.7951 (t80) REVERT: D 54 SER cc_start: 0.8176 (m) cc_final: 0.7975 (p) REVERT: D 259 ARG cc_start: 0.7340 (mtp180) cc_final: 0.6979 (mtp180) REVERT: E 174 ARG cc_start: 0.7620 (mtp-110) cc_final: 0.7254 (mtp85) REVERT: E 312 ILE cc_start: 0.8335 (pt) cc_final: 0.7939 (mm) outliers start: 40 outliers final: 29 residues processed: 233 average time/residue: 0.2602 time to fit residues: 92.4151 Evaluate side-chains 207 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL 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 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 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 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 227 MET Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 306 LEU 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 29 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 259 VAL 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 133 optimal weight: 0.0030 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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 C 208 HIS ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128606 restraints weight = 18644.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.131550 restraints weight = 10772.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133494 restraints weight = 7280.548| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13862 Z= 0.138 Angle : 0.645 11.101 18878 Z= 0.316 Chirality : 0.045 0.339 2183 Planarity : 0.004 0.043 2335 Dihedral : 7.033 101.442 2005 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.75 % Allowed : 16.01 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.21), residues: 1666 helix: 1.12 (0.21), residues: 574 sheet: -2.17 (0.26), residues: 371 loop : -1.92 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 177 HIS 0.005 0.001 HIS C 208 PHE 0.019 0.001 PHE B 107 TYR 0.026 0.001 TYR E 325 ARG 0.003 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 9) link_NAG-ASN : angle 4.14651 ( 27) hydrogen bonds : bond 0.03804 ( 670) hydrogen bonds : angle 4.71671 ( 2256) SS BOND : bond 0.00341 ( 8) SS BOND : angle 1.94218 ( 16) covalent geometry : bond 0.00314 (13845) covalent geometry : angle 0.62411 (18835) *********************** 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 241 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7198 (p0) cc_final: 0.6766 (p0) REVERT: A 154 MET cc_start: 0.8683 (mpp) cc_final: 0.7932 (ptp) REVERT: A 157 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7237 (mm-40) REVERT: B 96 MET cc_start: 0.7770 (ppp) cc_final: 0.7421 (ppp) REVERT: B 140 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 246 TRP cc_start: 0.8265 (m-10) cc_final: 0.7772 (m-10) REVERT: C 57 SER cc_start: 0.8979 (m) cc_final: 0.8457 (t) REVERT: C 64 ASP cc_start: 0.8183 (p0) cc_final: 0.7932 (p0) REVERT: C 250 TRP cc_start: 0.8115 (m100) cc_final: 0.7869 (m100) REVERT: C 308 TYR cc_start: 0.8346 (t80) cc_final: 0.7685 (t80) REVERT: D 226 GLN cc_start: 0.7789 (mt0) cc_final: 0.7312 (mm110) REVERT: D 259 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6897 (mtp180) REVERT: E 174 ARG cc_start: 0.7501 (mtp-110) cc_final: 0.7036 (mtp85) REVERT: E 237 ILE cc_start: 0.8990 (mt) cc_final: 0.8769 (mt) outliers start: 40 outliers final: 30 residues processed: 225 average time/residue: 0.2681 time to fit residues: 91.1646 Evaluate side-chains 205 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 224 GLU 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 167 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 281 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.142751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125875 restraints weight = 18674.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128763 restraints weight = 10867.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130672 restraints weight = 7382.707| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13862 Z= 0.167 Angle : 0.640 9.738 18878 Z= 0.314 Chirality : 0.044 0.230 2183 Planarity : 0.004 0.043 2335 Dihedral : 6.995 101.741 2005 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.40 % Allowed : 16.77 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1666 helix: 1.35 (0.21), residues: 570 sheet: -1.93 (0.25), residues: 392 loop : -1.83 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 246 HIS 0.002 0.001 HIS B 116 PHE 0.021 0.002 PHE D 313 TYR 0.030 0.001 TYR E 325 ARG 0.007 0.000 ARG B 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 9) link_NAG-ASN : angle 3.68902 ( 27) hydrogen bonds : bond 0.03744 ( 670) hydrogen bonds : angle 4.61288 ( 2256) SS BOND : bond 0.00289 ( 8) SS BOND : angle 1.68205 ( 16) covalent geometry : bond 0.00392 (13845) covalent geometry : angle 0.62390 (18835) *********************** 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 263 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.7006 (p0) cc_final: 0.6687 (p0) REVERT: A 154 MET cc_start: 0.8718 (mpp) cc_final: 0.7884 (ptp) REVERT: A 157 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7250 (mm-40) REVERT: A 202 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 206 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8935 (t) REVERT: B 96 MET cc_start: 0.7618 (ppp) cc_final: 0.7386 (ppp) REVERT: B 140 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8657 (p) REVERT: B 246 TRP cc_start: 0.8310 (m-10) cc_final: 0.7871 (m-10) REVERT: C 57 SER cc_start: 0.9058 (m) cc_final: 0.8573 (t) REVERT: C 250 TRP cc_start: 0.8190 (m100) cc_final: 0.7907 (m100) REVERT: C 308 TYR cc_start: 0.8326 (t80) cc_final: 0.7761 (t80) REVERT: C 404 LEU cc_start: 0.8613 (tt) cc_final: 0.8316 (tt) REVERT: D 250 TRP cc_start: 0.7658 (m100) cc_final: 0.7047 (m100) REVERT: D 259 ARG cc_start: 0.7210 (mtp180) cc_final: 0.6950 (mtp180) REVERT: D 270 MET cc_start: 0.7993 (mmt) cc_final: 0.7783 (tpt) REVERT: D 302 PHE cc_start: 0.7696 (m-80) cc_final: 0.7447 (m-80) REVERT: E 174 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.7068 (mtp85) REVERT: E 278 PRO cc_start: 0.8890 (Cg_exo) cc_final: 0.8547 (Cg_endo) outliers start: 64 outliers final: 47 residues processed: 243 average time/residue: 0.2266 time to fit residues: 83.9386 Evaluate side-chains 223 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 202 LEU 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 38 ASN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 176 GLU 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 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 61 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 205 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 156 VAL 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 391 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 39 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 120 optimal weight: 0.3980 chunk 70 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN C 273 GLN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127591 restraints weight = 18760.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130393 restraints weight = 10868.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132333 restraints weight = 7444.714| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13862 Z= 0.132 Angle : 0.617 8.906 18878 Z= 0.301 Chirality : 0.043 0.205 2183 Planarity : 0.004 0.037 2335 Dihedral : 6.845 104.743 2005 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.19 % Allowed : 17.94 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1666 helix: 1.48 (0.21), residues: 574 sheet: -1.75 (0.24), residues: 434 loop : -1.67 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 246 HIS 0.002 0.000 HIS B 116 PHE 0.022 0.001 PHE D 313 TYR 0.033 0.001 TYR E 325 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 9) link_NAG-ASN : angle 3.28040 ( 27) hydrogen bonds : bond 0.03541 ( 670) hydrogen bonds : angle 4.44050 ( 2256) SS BOND : bond 0.00311 ( 8) SS BOND : angle 2.00401 ( 16) covalent geometry : bond 0.00301 (13845) covalent geometry : angle 0.60271 (18835) *********************** 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 249 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 188 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7560 (mtp) cc_final: 0.7183 (ttm) REVERT: A 117 ASP cc_start: 0.7258 (p0) cc_final: 0.6955 (p0) REVERT: A 154 MET cc_start: 0.8690 (mpp) cc_final: 0.7926 (ptp) REVERT: A 206 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.8914 (t) REVERT: B 140 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8739 (p) REVERT: B 246 TRP cc_start: 0.8206 (m-10) cc_final: 0.7792 (m-10) REVERT: C 57 SER cc_start: 0.9090 (m) cc_final: 0.8658 (t) REVERT: C 73 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: C 233 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7422 (tm-30) REVERT: C 250 TRP cc_start: 0.8190 (m100) cc_final: 0.7924 (m100) REVERT: C 308 TYR cc_start: 0.8258 (t80) cc_final: 0.7728 (t80) REVERT: C 404 LEU cc_start: 0.8583 (tt) cc_final: 0.8289 (tt) REVERT: D 226 GLN cc_start: 0.7822 (mt0) cc_final: 0.7458 (mm110) REVERT: D 250 TRP cc_start: 0.7632 (m100) cc_final: 0.7030 (m100) REVERT: D 259 ARG cc_start: 0.7157 (mtp180) cc_final: 0.6917 (mtp180) REVERT: D 277 SER cc_start: 0.8430 (m) cc_final: 0.8161 (t) REVERT: D 302 PHE cc_start: 0.7726 (m-80) cc_final: 0.7433 (m-80) REVERT: E 116 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8515 (pp) REVERT: E 174 ARG cc_start: 0.7500 (mtp-110) cc_final: 0.7057 (mtp85) outliers start: 61 outliers final: 48 residues processed: 228 average time/residue: 0.2415 time to fit residues: 83.8630 Evaluate side-chains 219 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 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 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 239 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 96 MET 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 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 391 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.145290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128155 restraints weight = 18794.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131081 restraints weight = 10930.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133005 restraints weight = 7450.590| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13862 Z= 0.127 Angle : 0.603 8.224 18878 Z= 0.297 Chirality : 0.043 0.201 2183 Planarity : 0.004 0.038 2335 Dihedral : 6.699 105.131 2005 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.05 % Allowed : 18.42 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1666 helix: 1.53 (0.21), residues: 574 sheet: -1.61 (0.24), residues: 434 loop : -1.62 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 246 HIS 0.002 0.000 HIS B 116 PHE 0.022 0.001 PHE D 313 TYR 0.030 0.001 TYR E 325 ARG 0.007 0.000 ARG B 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 9) link_NAG-ASN : angle 3.05733 ( 27) hydrogen bonds : bond 0.03469 ( 670) hydrogen bonds : angle 4.37259 ( 2256) SS BOND : bond 0.00274 ( 8) SS BOND : angle 1.90541 ( 16) covalent geometry : bond 0.00291 (13845) covalent geometry : angle 0.58980 (18835) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 182 time to evaluate : 1.734 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: 0.8658 (mpp) cc_final: 0.7817 (ptp) REVERT: B 140 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8728 (p) REVERT: B 246 TRP cc_start: 0.8136 (m-10) cc_final: 0.7746 (m-10) REVERT: C 57 SER cc_start: 0.9087 (m) cc_final: 0.8668 (t) REVERT: C 62 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8623 (p) REVERT: C 73 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8153 (pt0) REVERT: C 154 MET cc_start: 0.7479 (mtm) cc_final: 0.7164 (mpp) REVERT: C 233 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 250 TRP cc_start: 0.8275 (m100) cc_final: 0.7909 (m100) REVERT: C 308 TYR cc_start: 0.8203 (t80) cc_final: 0.7683 (t80) REVERT: C 404 LEU cc_start: 0.8617 (tt) cc_final: 0.8339 (tt) REVERT: D 54 SER cc_start: 0.8241 (m) cc_final: 0.7962 (t) REVERT: D 226 GLN cc_start: 0.7824 (mt0) cc_final: 0.7476 (mm110) REVERT: D 250 TRP cc_start: 0.7611 (m100) cc_final: 0.7070 (m100) REVERT: D 277 SER cc_start: 0.8481 (m) cc_final: 0.8110 (t) REVERT: D 302 PHE cc_start: 0.7682 (m-80) cc_final: 0.7460 (m-80) REVERT: E 116 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8504 (pp) REVERT: E 174 ARG cc_start: 0.7499 (mtp-110) cc_final: 0.6890 (mtp85) outliers start: 59 outliers final: 45 residues processed: 223 average time/residue: 0.2161 time to fit residues: 74.6819 Evaluate side-chains 217 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 292 ILE Chi-restraints excluded: chain A residue 300 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 148 ASP 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 262 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 62 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 C residue 312 ASN Chi-restraints excluded: chain D residue 62 THR 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 156 VAL Chi-restraints excluded: chain D residue 205 CYS 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 E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 LEU 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 265 SER Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** D 157 GLN E 67 ASN E 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126697 restraints weight = 18749.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129606 restraints weight = 10845.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131294 restraints weight = 7357.132| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13862 Z= 0.141 Angle : 0.610 8.012 18878 Z= 0.299 Chirality : 0.043 0.205 2183 Planarity : 0.004 0.038 2335 Dihedral : 6.608 103.885 2005 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.60 % Allowed : 18.69 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1666 helix: 1.55 (0.21), residues: 574 sheet: -1.49 (0.24), residues: 434 loop : -1.57 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP A 246 HIS 0.002 0.001 HIS B 116 PHE 0.025 0.001 PHE D 313 TYR 0.026 0.001 TYR E 325 ARG 0.002 0.000 ARG B 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 9) link_NAG-ASN : angle 2.95387 ( 27) hydrogen bonds : bond 0.03456 ( 670) hydrogen bonds : angle 4.36761 ( 2256) SS BOND : bond 0.00246 ( 8) SS BOND : angle 1.85869 ( 16) covalent geometry : bond 0.00327 (13845) covalent geometry : angle 0.59751 (18835) *********************** 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 249 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 182 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8692 (mpp) cc_final: 0.7852 (ptp) REVERT: A 206 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8885 (t) REVERT: B 140 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8613 (p) REVERT: B 246 TRP cc_start: 0.8165 (m-10) cc_final: 0.7797 (m-10) REVERT: C 57 SER cc_start: 0.9111 (m) cc_final: 0.8677 (t) REVERT: C 62 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8614 (p) REVERT: C 73 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8197 (pt0) REVERT: C 154 MET cc_start: 0.7517 (mtm) cc_final: 0.7235 (mpp) REVERT: C 233 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7879 (tm-30) REVERT: C 250 TRP cc_start: 0.8258 (m100) cc_final: 0.7892 (m100) REVERT: C 308 TYR cc_start: 0.8184 (t80) cc_final: 0.7623 (t80) REVERT: C 404 LEU cc_start: 0.8642 (tt) cc_final: 0.8366 (tt) REVERT: D 226 GLN cc_start: 0.7824 (mt0) cc_final: 0.7547 (mm110) REVERT: D 250 TRP cc_start: 0.7631 (m100) cc_final: 0.7019 (m100) REVERT: D 259 ARG cc_start: 0.7227 (mtp180) cc_final: 0.6987 (mtp180) REVERT: D 277 SER cc_start: 0.8362 (m) cc_final: 0.8022 (t) REVERT: D 302 PHE cc_start: 0.7655 (m-80) cc_final: 0.7450 (m-80) REVERT: E 116 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8502 (pp) REVERT: E 174 ARG cc_start: 0.7552 (mtp-110) cc_final: 0.7010 (mtp85) outliers start: 67 outliers final: 53 residues processed: 225 average time/residue: 0.2186 time to fit residues: 76.2761 Evaluate side-chains 233 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 175 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 272 THR 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 148 ASP 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 262 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 62 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 299 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 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 E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL 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 265 SER Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 461 PHE Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 55 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.144306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127242 restraints weight = 18793.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130060 restraints weight = 10930.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132016 restraints weight = 7472.216| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 0.056 13862 Z= 0.135 Angle : 0.605 7.917 18878 Z= 0.297 Chirality : 0.043 0.204 2183 Planarity : 0.004 0.041 2335 Dihedral : 6.545 103.201 2005 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.05 % Allowed : 19.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1666 helix: 1.62 (0.21), residues: 574 sheet: -1.42 (0.24), residues: 434 loop : -1.49 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP A 246 HIS 0.002 0.000 HIS B 116 PHE 0.026 0.001 PHE D 313 TYR 0.030 0.001 TYR E 113 ARG 0.002 0.000 ARG E 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 9) link_NAG-ASN : angle 2.82538 ( 27) hydrogen bonds : bond 0.03452 ( 670) hydrogen bonds : angle 4.36340 ( 2256) SS BOND : bond 0.00249 ( 8) SS BOND : angle 1.72546 ( 16) covalent geometry : bond 0.00311 (13845) covalent geometry : angle 0.59449 (18835) *********************** 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 248 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 1.551 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: 0.8694 (mpp) cc_final: 0.7844 (ptp) REVERT: A 206 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8886 (t) REVERT: B 140 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8579 (p) REVERT: B 246 TRP cc_start: 0.8134 (m-10) cc_final: 0.7790 (m-10) REVERT: C 57 SER cc_start: 0.9123 (m) cc_final: 0.8684 (t) REVERT: C 62 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8627 (p) REVERT: C 73 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8202 (pt0) REVERT: C 154 MET cc_start: 0.7449 (mtm) cc_final: 0.7211 (mpp) REVERT: C 180 ASP cc_start: 0.6888 (p0) cc_final: 0.6643 (p0) REVERT: C 233 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7910 (tm-30) REVERT: C 250 TRP cc_start: 0.8254 (m100) cc_final: 0.7906 (m100) REVERT: C 404 LEU cc_start: 0.8623 (tt) cc_final: 0.8337 (tt) REVERT: D 54 SER cc_start: 0.8238 (m) cc_final: 0.7907 (t) REVERT: D 226 GLN cc_start: 0.7890 (mt0) cc_final: 0.7570 (mm110) REVERT: D 250 TRP cc_start: 0.7638 (m100) cc_final: 0.7093 (m100) REVERT: E 116 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8514 (pp) REVERT: E 174 ARG cc_start: 0.7595 (mtp-110) cc_final: 0.7230 (mtp85) outliers start: 59 outliers final: 51 residues processed: 227 average time/residue: 0.2229 time to fit residues: 78.8156 Evaluate side-chains 231 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 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 148 ASP 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 262 LEU Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 62 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 299 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain D residue 62 THR 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 156 VAL 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 E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL 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 265 SER Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 461 PHE Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN 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 = 0.3647 r_free = 0.3647 target = 0.146445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129310 restraints weight = 18777.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132258 restraints weight = 10889.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134126 restraints weight = 7387.096| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13862 Z= 0.115 Angle : 0.602 9.002 18878 Z= 0.294 Chirality : 0.043 0.190 2183 Planarity : 0.004 0.044 2335 Dihedral : 6.391 102.145 2005 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.64 % Allowed : 20.62 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1666 helix: 1.68 (0.22), residues: 574 sheet: -1.32 (0.24), residues: 434 loop : -1.38 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP A 246 HIS 0.002 0.000 HIS B 116 PHE 0.026 0.001 PHE D 313 TYR 0.024 0.001 TYR E 113 ARG 0.002 0.000 ARG D 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 9) link_NAG-ASN : angle 2.55670 ( 27) hydrogen bonds : bond 0.03344 ( 670) hydrogen bonds : angle 4.30184 ( 2256) SS BOND : bond 0.00262 ( 8) SS BOND : angle 1.65324 ( 16) covalent geometry : bond 0.00259 (13845) covalent geometry : angle 0.59254 (18835) *********************** 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 251 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7086 (p0) cc_final: 0.6634 (p0) REVERT: A 154 MET cc_start: 0.8644 (mpp) cc_final: 0.7798 (ptp) REVERT: A 206 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8868 (t) REVERT: B 140 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8500 (p) REVERT: C 57 SER cc_start: 0.9127 (m) cc_final: 0.8684 (t) REVERT: C 73 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: C 180 ASP cc_start: 0.6874 (p0) cc_final: 0.6624 (p0) REVERT: C 233 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7948 (tm-30) REVERT: C 250 TRP cc_start: 0.8216 (m100) cc_final: 0.7873 (m100) REVERT: C 312 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7559 (m110) REVERT: C 404 LEU cc_start: 0.8614 (tt) cc_final: 0.8358 (tt) REVERT: D 54 SER cc_start: 0.8136 (m) cc_final: 0.7826 (t) REVERT: D 226 GLN cc_start: 0.7899 (mt0) cc_final: 0.7550 (mm110) REVERT: D 250 TRP cc_start: 0.7614 (m100) cc_final: 0.7080 (m100) REVERT: E 116 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8530 (pp) REVERT: E 126 GLU cc_start: 0.7536 (tt0) cc_final: 0.7305 (tt0) REVERT: E 174 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7214 (mtp85) REVERT: E 243 GLN cc_start: 0.9098 (pm20) cc_final: 0.8743 (pm20) outliers start: 53 outliers final: 46 residues processed: 235 average time/residue: 0.2153 time to fit residues: 78.3394 Evaluate side-chains 232 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 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 239 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 205 CYS 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 E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL 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 301 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 461 PHE Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 59 optimal weight: 0.0020 chunk 157 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.151024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133896 restraints weight = 18530.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.136849 restraints weight = 10794.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138733 restraints weight = 7371.776| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13862 Z= 0.113 Angle : 0.609 9.661 18878 Z= 0.297 Chirality : 0.043 0.240 2183 Planarity : 0.004 0.055 2335 Dihedral : 6.245 100.662 2005 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.23 % Allowed : 21.37 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1666 helix: 1.75 (0.22), residues: 574 sheet: -1.14 (0.26), residues: 393 loop : -1.42 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 246 HIS 0.002 0.000 HIS C 116 PHE 0.035 0.001 PHE B 313 TYR 0.026 0.001 TYR A 308 ARG 0.002 0.000 ARG A 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 9) link_NAG-ASN : angle 2.36586 ( 27) hydrogen bonds : bond 0.03309 ( 670) hydrogen bonds : angle 4.28502 ( 2256) SS BOND : bond 0.00255 ( 8) SS BOND : angle 1.56720 ( 16) covalent geometry : bond 0.00248 (13845) covalent geometry : angle 0.60140 (18835) ********************** 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 247 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7065 (p0) cc_final: 0.6634 (p0) REVERT: A 154 MET cc_start: 0.8602 (mpp) cc_final: 0.7766 (ptp) REVERT: A 206 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8859 (t) REVERT: B 140 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8628 (p) REVERT: C 21 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8370 (mp) REVERT: C 57 SER cc_start: 0.9093 (m) cc_final: 0.8681 (t) REVERT: C 73 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: C 180 ASP cc_start: 0.6831 (p0) cc_final: 0.6586 (p0) REVERT: C 233 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7952 (tm-30) REVERT: C 250 TRP cc_start: 0.8238 (m100) cc_final: 0.7871 (m100) REVERT: C 404 LEU cc_start: 0.8635 (tt) cc_final: 0.8374 (tt) REVERT: D 54 SER cc_start: 0.8042 (m) cc_final: 0.7777 (t) REVERT: D 226 GLN cc_start: 0.7881 (mt0) cc_final: 0.7582 (mm110) REVERT: D 250 TRP cc_start: 0.7622 (m100) cc_final: 0.7037 (m100) REVERT: D 259 ARG cc_start: 0.7295 (mtp180) cc_final: 0.6899 (mtp180) REVERT: E 174 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.7134 (mtp85) outliers start: 47 outliers final: 36 residues processed: 232 average time/residue: 0.2167 time to fit residues: 77.7773 Evaluate side-chains 225 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 300 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 262 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 76 THR 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 301 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 461 PHE Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 312 ASN C 312 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133055 restraints weight = 18502.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135953 restraints weight = 10808.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137867 restraints weight = 7411.604| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13862 Z= 0.122 Angle : 0.622 9.370 18878 Z= 0.301 Chirality : 0.044 0.284 2183 Planarity : 0.004 0.054 2335 Dihedral : 6.175 98.745 2005 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.23 % Allowed : 21.92 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1666 helix: 1.81 (0.22), residues: 574 sheet: -1.12 (0.26), residues: 395 loop : -1.37 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 246 HIS 0.002 0.000 HIS B 116 PHE 0.027 0.001 PHE D 313 TYR 0.027 0.001 TYR A 308 ARG 0.002 0.000 ARG D 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 9) link_NAG-ASN : angle 2.36382 ( 27) hydrogen bonds : bond 0.03317 ( 670) hydrogen bonds : angle 4.26760 ( 2256) SS BOND : bond 0.00317 ( 8) SS BOND : angle 1.61522 ( 16) covalent geometry : bond 0.00278 (13845) covalent geometry : angle 0.61418 (18835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4002.39 seconds wall clock time: 72 minutes 29.97 seconds (4349.97 seconds total)