Starting phenix.real_space_refine on Thu Sep 26 14:41:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkg_9404/09_2024/5bkg_9404.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkg_9404/09_2024/5bkg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkg_9404/09_2024/5bkg_9404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkg_9404/09_2024/5bkg_9404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkg_9404/09_2024/5bkg_9404.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkg_9404/09_2024/5bkg_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-5461/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: 8.20, per 1000 atoms: 0.61 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: 3.21 Conformation dependent library (CDL) restraints added in 1.6 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: 4.31 Time building geometry restraints manager: 3.75 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: 1.400 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.400 Find NCS groups from input model: 0.640 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- 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 13845 Z= 0.282 Angle : 0.579 5.837 18835 Z= 0.330 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 279 time to evaluate : 1.565 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: 0.2340 time to fit residues: 97.0349 Evaluate side-chains 185 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 13845 Z= 0.442 Angle : 0.761 10.874 18835 Z= 0.383 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 *********************** 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 fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7335 (p0) cc_final: 0.6939 (p0) REVERT: A 157 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7424 (mm-40) REVERT: A 246 TRP cc_start: 0.8284 (m-10) cc_final: 0.8067 (m-10) REVERT: A 415 LYS cc_start: 0.8239 (tppp) cc_final: 0.7914 (ttpt) REVERT: B 109 ASN cc_start: 0.8584 (p0) cc_final: 0.7893 (p0) REVERT: B 246 TRP cc_start: 0.8439 (m-10) cc_final: 0.7856 (m-10) REVERT: C 57 SER cc_start: 0.8981 (m) cc_final: 0.8373 (t) REVERT: C 64 ASP cc_start: 0.8311 (p0) cc_final: 0.8022 (p0) REVERT: C 250 TRP cc_start: 0.8156 (m100) cc_final: 0.7732 (m100) REVERT: C 308 TYR cc_start: 0.8536 (t80) cc_final: 0.7979 (t80) REVERT: D 68 ASN cc_start: 0.8471 (p0) cc_final: 0.8217 (p0) REVERT: D 259 ARG cc_start: 0.7345 (mtp180) cc_final: 0.6968 (mtp180) REVERT: E 133 ASP cc_start: 0.7369 (p0) cc_final: 0.7130 (p0) REVERT: E 174 ARG cc_start: 0.7639 (mtp-110) cc_final: 0.7270 (mtp85) REVERT: E 312 ILE cc_start: 0.8320 (pt) cc_final: 0.7929 (mm) outliers start: 40 outliers final: 29 residues processed: 233 average time/residue: 0.2199 time to fit residues: 77.4010 Evaluate side-chains 208 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13845 Z= 0.222 Angle : 0.624 8.034 18835 Z= 0.311 Chirality : 0.045 0.310 2183 Planarity : 0.004 0.043 2335 Dihedral : 6.934 96.648 2005 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.82 % Allowed : 16.22 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.21), residues: 1666 helix: 1.12 (0.21), residues: 574 sheet: -2.12 (0.24), residues: 407 loop : -1.92 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 177 HIS 0.004 0.001 HIS C 208 PHE 0.019 0.002 PHE A 406 TYR 0.025 0.001 TYR E 325 ARG 0.004 0.000 ARG D 66 *********************** 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 245 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7244 (p0) cc_final: 0.6835 (p0) REVERT: A 154 MET cc_start: 0.8696 (mpp) cc_final: 0.7954 (ptp) REVERT: A 157 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7269 (mm-40) REVERT: B 96 MET cc_start: 0.7771 (ppp) cc_final: 0.7400 (ppp) REVERT: B 140 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8566 (p) REVERT: B 246 TRP cc_start: 0.8292 (m-10) cc_final: 0.7753 (m-10) REVERT: C 57 SER cc_start: 0.8977 (m) cc_final: 0.8427 (t) REVERT: C 64 ASP cc_start: 0.8192 (p0) cc_final: 0.7967 (p0) REVERT: C 250 TRP cc_start: 0.8153 (m100) cc_final: 0.7873 (m100) REVERT: C 308 TYR cc_start: 0.8357 (t80) cc_final: 0.7753 (t80) REVERT: D 251 ILE cc_start: 0.8704 (mt) cc_final: 0.8502 (mt) REVERT: D 259 ARG cc_start: 0.7206 (mtp180) cc_final: 0.6916 (mtp180) REVERT: E 133 ASP cc_start: 0.7315 (p0) cc_final: 0.7043 (p0) REVERT: E 174 ARG cc_start: 0.7528 (mtp-110) cc_final: 0.7058 (mtp85) REVERT: E 237 ILE cc_start: 0.9010 (mt) cc_final: 0.8809 (mt) outliers start: 41 outliers final: 29 residues processed: 229 average time/residue: 0.2295 time to fit residues: 78.8617 Evaluate side-chains 209 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 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 183 VAL Chi-restraints excluded: chain B residue 193 GLN 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 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 224 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 264 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 77 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN B 312 ASN C 273 GLN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13845 Z= 0.170 Angle : 0.593 8.349 18835 Z= 0.294 Chirality : 0.043 0.236 2183 Planarity : 0.004 0.039 2335 Dihedral : 6.785 100.657 2005 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.44 % Allowed : 17.53 % Favored : 79.04 % 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: -1.01 (0.21), residues: 1666 helix: 1.45 (0.21), residues: 574 sheet: -1.82 (0.26), residues: 382 loop : -1.76 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 246 HIS 0.002 0.000 HIS B 116 PHE 0.020 0.001 PHE D 313 TYR 0.027 0.001 TYR E 325 ARG 0.007 0.000 ARG B 36 *********************** 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 252 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 202 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.6808 (p0) cc_final: 0.6475 (p0) REVERT: A 154 MET cc_start: 0.8674 (mpp) cc_final: 0.7869 (ptp) REVERT: A 157 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7186 (mm-40) REVERT: A 206 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8821 (t) REVERT: B 96 MET cc_start: 0.7626 (ppp) cc_final: 0.7345 (ppp) REVERT: B 126 ARG cc_start: 0.8565 (ttm110) cc_final: 0.8132 (mtp-110) REVERT: B 140 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8589 (p) REVERT: B 246 TRP cc_start: 0.8151 (m-10) cc_final: 0.7698 (m-10) REVERT: C 57 SER cc_start: 0.9008 (m) cc_final: 0.8479 (t) REVERT: C 64 ASP cc_start: 0.8185 (p0) cc_final: 0.7968 (p0) REVERT: C 250 TRP cc_start: 0.8181 (m100) cc_final: 0.7853 (m100) REVERT: C 308 TYR cc_start: 0.8211 (t80) cc_final: 0.7718 (t80) REVERT: C 404 LEU cc_start: 0.8541 (tt) cc_final: 0.8251 (tt) REVERT: D 226 GLN cc_start: 0.7755 (mt0) cc_final: 0.7466 (mm110) REVERT: D 250 TRP cc_start: 0.7630 (m100) cc_final: 0.7044 (m100) REVERT: D 259 ARG cc_start: 0.7174 (mtp180) cc_final: 0.6888 (mtp180) REVERT: D 277 SER cc_start: 0.8385 (m) cc_final: 0.7751 (p) REVERT: D 302 PHE cc_start: 0.7799 (m-80) cc_final: 0.7467 (m-80) REVERT: E 116 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8407 (pp) REVERT: E 174 ARG cc_start: 0.7458 (mtp-110) cc_final: 0.6826 (mtp85) REVERT: E 237 ILE cc_start: 0.8961 (mt) cc_final: 0.8759 (mt) REVERT: E 278 PRO cc_start: 0.8837 (Cg_exo) cc_final: 0.8525 (Cg_endo) outliers start: 50 outliers final: 31 residues processed: 238 average time/residue: 0.2255 time to fit residues: 80.7236 Evaluate side-chains 210 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 140 THR 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 205 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 148 ASP Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain E residue 29 VAL 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 264 LEU Chi-restraints excluded: chain E residue 265 SER 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 132 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 0.0970 chunk 65 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- 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 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13845 Z= 0.344 Angle : 0.674 9.062 18835 Z= 0.333 Chirality : 0.045 0.234 2183 Planarity : 0.004 0.036 2335 Dihedral : 6.920 101.391 2005 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.81 % Allowed : 17.46 % Favored : 77.73 % 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: -1.08 (0.21), residues: 1666 helix: 1.38 (0.21), residues: 570 sheet: -1.80 (0.24), residues: 426 loop : -1.78 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 246 HIS 0.002 0.001 HIS B 116 PHE 0.022 0.002 PHE D 313 TYR 0.020 0.002 TYR C 135 ARG 0.003 0.000 ARG B 36 *********************** 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 261 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 191 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.7023 (p0) cc_final: 0.6598 (p0) REVERT: A 117 ASP cc_start: 0.7374 (p0) cc_final: 0.7163 (p0) REVERT: A 154 MET cc_start: 0.8713 (mpp) cc_final: 0.8068 (ptp) REVERT: A 202 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7967 (mt) REVERT: A 206 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.8946 (t) REVERT: B 96 MET cc_start: 0.7797 (ppp) cc_final: 0.7483 (ppp) REVERT: B 246 TRP cc_start: 0.8370 (m-10) cc_final: 0.7979 (m-10) REVERT: C 57 SER cc_start: 0.9077 (m) cc_final: 0.8566 (t) REVERT: C 233 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7484 (tm-30) REVERT: C 250 TRP cc_start: 0.8175 (m100) cc_final: 0.7885 (m100) REVERT: C 308 TYR cc_start: 0.8349 (t80) cc_final: 0.7830 (t80) REVERT: D 171 ASN cc_start: 0.7708 (t0) cc_final: 0.7500 (m-40) REVERT: D 226 GLN cc_start: 0.7871 (mt0) cc_final: 0.7549 (mm110) REVERT: D 250 TRP cc_start: 0.7639 (m100) cc_final: 0.7047 (m100) REVERT: D 259 ARG cc_start: 0.7312 (mtp180) cc_final: 0.7093 (mtp180) REVERT: D 302 PHE cc_start: 0.7820 (m-80) cc_final: 0.7543 (m-80) REVERT: D 307 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8568 (tm-30) REVERT: E 126 GLU cc_start: 0.7960 (tt0) cc_final: 0.7734 (tt0) REVERT: E 174 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7030 (mtp85) REVERT: E 278 PRO cc_start: 0.8859 (Cg_exo) cc_final: 0.8568 (Cg_endo) outliers start: 70 outliers final: 52 residues processed: 236 average time/residue: 0.2227 time to fit residues: 79.7233 Evaluate side-chains 235 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 181 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 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 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 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 287 VAL 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 96 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 96 MET 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 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 146 ASP 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 281 ILE Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 VAL 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 53 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** E 67 ASN E 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13845 Z= 0.336 Angle : 0.661 8.471 18835 Z= 0.329 Chirality : 0.046 0.239 2183 Planarity : 0.004 0.046 2335 Dihedral : 7.003 103.433 2005 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.50 % Allowed : 17.46 % Favored : 77.04 % 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: -1.04 (0.21), residues: 1666 helix: 1.33 (0.21), residues: 570 sheet: -1.67 (0.25), residues: 405 loop : -1.77 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 246 HIS 0.002 0.001 HIS B 116 PHE 0.023 0.002 PHE D 313 TYR 0.021 0.002 TYR E 113 ARG 0.008 0.000 ARG B 36 *********************** 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 263 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 183 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7405 (p0) cc_final: 0.7191 (p0) REVERT: A 154 MET cc_start: 0.8731 (mpp) cc_final: 0.8105 (ptp) REVERT: A 202 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8055 (mt) REVERT: A 206 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8935 (t) REVERT: B 96 MET cc_start: 0.7836 (ppp) cc_final: 0.7587 (ppp) REVERT: B 140 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8721 (p) REVERT: B 246 TRP cc_start: 0.8373 (m-10) cc_final: 0.7943 (m100) REVERT: C 57 SER cc_start: 0.9139 (m) cc_final: 0.8671 (t) REVERT: C 62 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8622 (p) REVERT: C 73 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8268 (pt0) REVERT: C 233 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7477 (tm-30) REVERT: C 250 TRP cc_start: 0.8327 (m100) cc_final: 0.7979 (m100) REVERT: D 226 GLN cc_start: 0.7948 (mt0) cc_final: 0.7513 (mm110) REVERT: D 250 TRP cc_start: 0.7635 (m100) cc_final: 0.7107 (m100) REVERT: D 277 SER cc_start: 0.7943 (t) cc_final: 0.7702 (p) REVERT: D 302 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: E 116 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8514 (pp) REVERT: E 126 GLU cc_start: 0.8087 (tt0) cc_final: 0.7866 (tt0) REVERT: E 174 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7386 (mtp85) REVERT: E 278 PRO cc_start: 0.8873 (Cg_exo) cc_final: 0.8581 (Cg_endo) outliers start: 80 outliers final: 62 residues processed: 239 average time/residue: 0.2213 time to fit residues: 80.5543 Evaluate side-chains 245 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 176 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 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 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 176 GLU 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 271 THR 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 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 271 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain D residue 54 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 215 THR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET 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 311 LEU Chi-restraints excluded: chain E residue 322 LEU 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 153 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13845 Z= 0.340 Angle : 0.663 8.187 18835 Z= 0.330 Chirality : 0.045 0.242 2183 Planarity : 0.004 0.038 2335 Dihedral : 7.041 103.817 2005 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.29 % Allowed : 18.56 % Favored : 76.15 % 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: -1.01 (0.21), residues: 1666 helix: 1.28 (0.21), residues: 570 sheet: -1.63 (0.25), residues: 415 loop : -1.70 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 246 HIS 0.002 0.001 HIS B 116 PHE 0.023 0.002 PHE D 313 TYR 0.022 0.002 TYR E 113 ARG 0.007 0.000 ARG B 36 *********************** 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 263 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 186 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7422 (p0) cc_final: 0.7191 (p0) REVERT: A 154 MET cc_start: 0.8741 (mpp) cc_final: 0.8136 (ptp) REVERT: A 202 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8138 (mt) REVERT: A 206 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.8976 (t) REVERT: A 391 ILE cc_start: 0.7410 (tp) cc_final: 0.7116 (tt) REVERT: B 96 MET cc_start: 0.7925 (ppp) cc_final: 0.7654 (ppp) REVERT: B 140 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8740 (p) REVERT: B 246 TRP cc_start: 0.8391 (m-10) cc_final: 0.8048 (m-10) REVERT: C 21 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8129 (mp) REVERT: C 62 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8621 (p) REVERT: C 73 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: C 233 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8007 (tm-30) REVERT: C 250 TRP cc_start: 0.8201 (m100) cc_final: 0.7902 (m100) REVERT: D 226 GLN cc_start: 0.7929 (mt0) cc_final: 0.7553 (mm110) REVERT: D 250 TRP cc_start: 0.7637 (m100) cc_final: 0.7130 (m100) REVERT: D 302 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: E 116 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8541 (pp) REVERT: E 126 GLU cc_start: 0.8236 (tt0) cc_final: 0.7800 (tt0) REVERT: E 174 ARG cc_start: 0.7718 (mtp-110) cc_final: 0.7450 (mtp85) REVERT: E 278 PRO cc_start: 0.8887 (Cg_exo) cc_final: 0.8619 (Cg_endo) outliers start: 77 outliers final: 61 residues processed: 239 average time/residue: 0.2196 time to fit residues: 79.6962 Evaluate side-chains 244 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 175 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 185 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 206 THR 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 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 271 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain C residue 21 LEU 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 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 268 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 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 D residue 302 PHE Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 83 ILE 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 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET 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 298 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 322 LEU 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 63 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13845 Z= 0.284 Angle : 0.651 7.987 18835 Z= 0.323 Chirality : 0.045 0.264 2183 Planarity : 0.004 0.041 2335 Dihedral : 6.957 104.140 2005 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.02 % Allowed : 19.59 % 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: -0.94 (0.21), residues: 1666 helix: 1.36 (0.21), residues: 570 sheet: -1.62 (0.24), residues: 418 loop : -1.64 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 246 HIS 0.002 0.001 HIS C 116 PHE 0.026 0.002 PHE D 313 TYR 0.020 0.001 TYR C 135 ARG 0.003 0.000 ARG B 36 *********************** 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 256 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 183 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7425 (p0) cc_final: 0.7201 (p0) REVERT: A 154 MET cc_start: 0.8725 (mpp) cc_final: 0.8120 (ptp) REVERT: A 206 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.8982 (t) REVERT: A 391 ILE cc_start: 0.7373 (tp) cc_final: 0.7077 (tt) REVERT: B 25 MET cc_start: 0.8470 (ptm) cc_final: 0.8196 (ptp) REVERT: B 140 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8705 (p) REVERT: B 246 TRP cc_start: 0.8370 (m-10) cc_final: 0.8045 (m-10) REVERT: C 57 SER cc_start: 0.9186 (m) cc_final: 0.8731 (t) REVERT: C 62 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8649 (p) REVERT: C 73 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: C 250 TRP cc_start: 0.8134 (m100) cc_final: 0.7799 (m100) REVERT: C 312 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7603 (t0) REVERT: D 226 GLN cc_start: 0.7944 (mt0) cc_final: 0.7587 (mm110) REVERT: D 250 TRP cc_start: 0.7646 (m100) cc_final: 0.7134 (m100) REVERT: D 302 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: E 116 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8538 (pp) REVERT: E 126 GLU cc_start: 0.8267 (tt0) cc_final: 0.7805 (tt0) REVERT: E 174 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.7482 (mtp85) REVERT: E 243 GLN cc_start: 0.9025 (pm20) cc_final: 0.8737 (pm20) REVERT: E 278 PRO cc_start: 0.8828 (Cg_exo) cc_final: 0.8566 (Cg_endo) outliers start: 73 outliers final: 58 residues processed: 236 average time/residue: 0.2125 time to fit residues: 77.2769 Evaluate side-chains 236 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 171 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 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 239 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain 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 74 GLN 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 268 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain D residue 54 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 215 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 29 VAL 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 146 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 322 LEU 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 152 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13845 Z= 0.228 Angle : 0.644 7.800 18835 Z= 0.318 Chirality : 0.045 0.267 2183 Planarity : 0.004 0.044 2335 Dihedral : 6.808 103.861 2005 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.60 % Allowed : 20.55 % 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: -0.80 (0.21), residues: 1666 helix: 1.46 (0.22), residues: 570 sheet: -1.53 (0.24), residues: 418 loop : -1.56 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 246 HIS 0.002 0.001 HIS C 116 PHE 0.026 0.001 PHE D 313 TYR 0.021 0.001 TYR E 113 ARG 0.002 0.000 ARG E 190 *********************** 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 256 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 189 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7401 (p0) cc_final: 0.6913 (p0) REVERT: A 154 MET cc_start: 0.8731 (mpp) cc_final: 0.8056 (ptp) REVERT: A 206 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8955 (t) REVERT: A 391 ILE cc_start: 0.7455 (tp) cc_final: 0.7161 (tt) REVERT: B 140 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8637 (p) REVERT: B 246 TRP cc_start: 0.8281 (m-10) cc_final: 0.8011 (m-10) REVERT: C 57 SER cc_start: 0.9178 (m) cc_final: 0.8735 (t) REVERT: C 62 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8634 (p) REVERT: C 73 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8278 (pt0) REVERT: C 180 ASP cc_start: 0.6931 (p0) cc_final: 0.6700 (p0) REVERT: C 250 TRP cc_start: 0.8112 (m100) cc_final: 0.7743 (m100) REVERT: C 312 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7544 (t0) REVERT: D 226 GLN cc_start: 0.7918 (mt0) cc_final: 0.7595 (mm110) REVERT: D 250 TRP cc_start: 0.7624 (m100) cc_final: 0.7130 (m100) REVERT: D 302 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: E 116 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8531 (pp) REVERT: E 126 GLU cc_start: 0.8238 (tt0) cc_final: 0.7774 (tt0) REVERT: E 243 GLN cc_start: 0.9047 (pm20) cc_final: 0.8682 (pm20) REVERT: E 278 PRO cc_start: 0.8751 (Cg_exo) cc_final: 0.8487 (Cg_endo) outliers start: 67 outliers final: 53 residues processed: 237 average time/residue: 0.2143 time to fit residues: 78.0167 Evaluate side-chains 234 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 174 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 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 176 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 271 THR 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 74 GLN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 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 D residue 292 ILE Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 232 THR 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 311 LEU 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: 0.0870 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13845 Z= 0.191 Angle : 0.630 9.050 18835 Z= 0.308 Chirality : 0.044 0.339 2183 Planarity : 0.004 0.048 2335 Dihedral : 6.617 102.844 2005 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.71 % Allowed : 21.58 % Favored : 74.71 % 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: -0.65 (0.21), residues: 1666 helix: 1.61 (0.22), residues: 566 sheet: -1.40 (0.24), residues: 418 loop : -1.50 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A 246 HIS 0.002 0.001 HIS C 116 PHE 0.027 0.001 PHE D 313 TYR 0.023 0.001 TYR A 308 ARG 0.002 0.000 ARG A 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 198 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.7349 (p0) cc_final: 0.6904 (p0) REVERT: A 154 MET cc_start: 0.8719 (mpp) cc_final: 0.8008 (ptp) REVERT: A 206 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8938 (t) REVERT: B 140 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8569 (p) REVERT: B 246 TRP cc_start: 0.8140 (m-10) cc_final: 0.7872 (m-10) REVERT: C 57 SER cc_start: 0.9204 (m) cc_final: 0.8774 (t) REVERT: C 73 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: C 180 ASP cc_start: 0.6945 (p0) cc_final: 0.6734 (p0) REVERT: C 233 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7928 (tm-30) REVERT: C 250 TRP cc_start: 0.8050 (m100) cc_final: 0.7634 (m100) REVERT: C 312 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7469 (m110) REVERT: C 404 LEU cc_start: 0.8663 (tt) cc_final: 0.8372 (tt) REVERT: D 226 GLN cc_start: 0.7855 (mt0) cc_final: 0.7580 (mm110) REVERT: D 250 TRP cc_start: 0.7616 (m100) cc_final: 0.7104 (m100) REVERT: E 116 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8523 (pp) REVERT: E 126 GLU cc_start: 0.8141 (tt0) cc_final: 0.7674 (tt0) REVERT: E 178 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8149 (pt0) REVERT: E 243 GLN cc_start: 0.9075 (pm20) cc_final: 0.8418 (pm20) outliers start: 54 outliers final: 43 residues processed: 236 average time/residue: 0.2021 time to fit residues: 75.1313 Evaluate side-chains 233 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 184 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 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 226 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 74 GLN 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 312 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 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 D residue 292 ILE 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 167 LEU Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 232 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.125164 restraints weight = 18821.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128047 restraints weight = 10956.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129839 restraints weight = 7470.931| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13845 Z= 0.207 Angle : 0.633 9.762 18835 Z= 0.309 Chirality : 0.044 0.337 2183 Planarity : 0.004 0.051 2335 Dihedral : 6.536 101.362 2005 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.44 % Allowed : 22.13 % Favored : 74.43 % 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: -0.55 (0.21), residues: 1666 helix: 1.64 (0.22), residues: 570 sheet: -1.35 (0.25), residues: 418 loop : -1.41 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 246 HIS 0.002 0.001 HIS B 116 PHE 0.027 0.001 PHE D 313 TYR 0.024 0.001 TYR C 308 ARG 0.002 0.000 ARG B 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.84 seconds wall clock time: 46 minutes 19.72 seconds (2779.72 seconds total)