Starting phenix.real_space_refine on Sun Feb 25 12:43:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/02_2024/8ssz_40752_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/02_2024/8ssz_40752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/02_2024/8ssz_40752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/02_2024/8ssz_40752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/02_2024/8ssz_40752_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/02_2024/8ssz_40752_trim_updated.pdb" } resolution = 2.64 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 S 138 5.16 5 Na 1 4.78 5 C 16816 2.51 5 N 4249 2.21 5 O 4916 1.98 5 H 25319 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51441 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 6401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6401 Classifications: {'peptide': 393} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 6197 Classifications: {'peptide': 384} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 362} Chain breaks: 1 Chain: "C" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 6197 Classifications: {'peptide': 384} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 362} Chain breaks: 1 Chain: "D" Number of atoms: 6401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6401 Classifications: {'peptide': 393} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 373} Chain breaks: 1 Chain: "E" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 6197 Classifications: {'peptide': 384} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 362} Chain breaks: 1 Chain: "F" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "G" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3267 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "H" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "I" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3267 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "J" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "K" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3267 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 53 Unusual residues: {' CA': 1, 'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 53 Unusual residues: {' CA': 1, 'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' NA': 1, 'OCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 22.57, per 1000 atoms: 0.44 Number of scatterers: 51441 At special positions: 0 Unit cell: (201.773, 154.297, 183.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 138 16.00 Na 1 11.00 O 4916 8.00 N 4249 7.00 C 16816 6.00 H 25319 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 199 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 147 " - pdb=" SG CYS K 202 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 701 " - " ASN A 31 " " NAG A 702 " - " ASN A 81 " " NAG A 703 " - " ASN A 148 " " NAG D 701 " - " ASN D 31 " " NAG D 702 " - " ASN D 81 " " NAG D 703 " - " ASN D 148 " " NAG L 1 " - " ASN B 143 " " NAG M 1 " - " ASN C 143 " " NAG N 1 " - " ASN E 143 " Time building additional restraints: 39.33 Conformation dependent library (CDL) restraints added in 5.2 seconds 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 55 sheets defined 26.4% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.69 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 218 through 234 removed outlier: 4.575A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.821A pdb=" N LEU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 248 through 268 Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 316 through 329 removed outlier: 5.633A pdb=" N VAL A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 539 through 598 Proline residue: A 594 - end of helix Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 210 through 226 removed outlier: 4.644A pdb=" N ILE B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Proline residue: B 219 - end of helix removed outlier: 3.660A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 240 through 261 Processing helix chain 'B' and resid 271 through 297 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 397 through 448 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.549A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 3.751A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 240 through 261 Processing helix chain 'C' and resid 271 through 297 Processing helix chain 'C' and resid 308 through 314 Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 397 through 448 Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 218 through 234 removed outlier: 4.641A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.915A pdb=" N LEU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 248 through 267 Processing helix chain 'D' and resid 279 through 305 Processing helix chain 'D' and resid 316 through 329 removed outlier: 6.328A pdb=" N VAL D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Proline residue: D 327 - end of helix Processing helix chain 'D' and resid 539 through 598 Proline residue: D 594 - end of helix Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.521A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix removed outlier: 3.645A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 240 through 261 Processing helix chain 'E' and resid 271 through 297 Processing helix chain 'E' and resid 308 through 322 removed outlier: 5.473A pdb=" N LEU E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Proline residue: E 319 - end of helix Processing helix chain 'E' and resid 397 through 447 Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 188 through 191 No H-bonds generated for 'chain 'F' and resid 188 through 191' Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 192 through 197 Proline residue: G 196 - end of helix No H-bonds generated for 'chain 'G' and resid 192 through 197' Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'I' and resid 30 through 32 No H-bonds generated for 'chain 'I' and resid 30 through 32' Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 192 through 195 No H-bonds generated for 'chain 'I' and resid 192 through 195' Processing helix chain 'J' and resid 85 through 87 No H-bonds generated for 'chain 'J' and resid 85 through 87' Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 188 through 193 Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 63 through 65 No H-bonds generated for 'chain 'K' and resid 63 through 65' Processing helix chain 'K' and resid 192 through 195 No H-bonds generated for 'chain 'K' and resid 192 through 195' Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.183A pdb=" N VAL A 36 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 166 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 38 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR A 58 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 51 Processing sheet with id= C, first strand: chain 'A' and resid 84 through 88 Processing sheet with id= D, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.378A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.395A pdb=" N VAL B 31 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 33 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR B 32 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU B 63 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN B 55 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= G, first strand: chain 'B' and resid 79 through 83 Processing sheet with id= H, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.068A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 178 through 182 removed outlier: 6.811A pdb=" N ILE B 204 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.491A pdb=" N VAL C 31 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL C 33 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU C 121 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN C 109 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 44 through 46 Processing sheet with id= L, first strand: chain 'C' and resid 92 through 94 Processing sheet with id= M, first strand: chain 'C' and resid 178 through 182 removed outlier: 6.787A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.239A pdb=" N VAL D 36 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL D 166 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 38 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR D 58 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 49 through 51 Processing sheet with id= P, first strand: chain 'D' and resid 84 through 88 Processing sheet with id= Q, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.423A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 158 through 162 removed outlier: 6.506A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR E 32 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU E 63 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN E 55 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU E 42 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR E 53 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 44 through 46 Processing sheet with id= T, first strand: chain 'E' and resid 79 through 83 Processing sheet with id= U, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.300A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 178 through 182 removed outlier: 6.906A pdb=" N ILE E 204 " --> pdb=" O VAL E 181 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 4 through 7 Processing sheet with id= X, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.617A pdb=" N LYS F 108 " --> pdb=" O LEU F 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 90 through 95 removed outlier: 5.929A pdb=" N LEU F 42 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU F 51 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.705A pdb=" N ASN F 142 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 150 through 152 removed outlier: 3.576A pdb=" N ASN F 150 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 196 through 198 Processing sheet with id= AC, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.006A pdb=" N THR G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.534A pdb=" N MET G 13 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS G 39 " --> pdb=" O ARG G 48 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ARG G 48 " --> pdb=" O LYS G 39 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 127 through 130 removed outlier: 6.506A pdb=" N TYR G 182 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.572A pdb=" N VAL G 143 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 158 through 160 Processing sheet with id= AH, first strand: chain 'H' and resid 4 through 7 Processing sheet with id= AI, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.412A pdb=" N LYS H 108 " --> pdb=" O LEU H 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'H' and resid 90 through 95 removed outlier: 6.292A pdb=" N LEU H 42 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU H 51 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.573A pdb=" N VAL H 138 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 137 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 149 through 152 Processing sheet with id= AM, first strand: chain 'H' and resid 196 through 198 Processing sheet with id= AN, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.535A pdb=" N VAL I 19 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 11 through 13 removed outlier: 3.610A pdb=" N GLY I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS I 39 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ARG I 48 " --> pdb=" O LYS I 39 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 142 through 144 removed outlier: 3.706A pdb=" N VAL I 143 " --> pdb=" O VAL I 190 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 170 through 172 removed outlier: 3.760A pdb=" N SER I 187 " --> pdb=" O HIS I 171 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR I 152 " --> pdb=" O TYR I 182 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU I 184 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS I 150 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N SER I 186 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU I 148 " --> pdb=" O SER I 186 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 201 through 206 removed outlier: 4.395A pdb=" N CYS I 202 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS I 215 " --> pdb=" O CYS I 202 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'J' and resid 4 through 7 Processing sheet with id= AT, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.316A pdb=" N LYS J 108 " --> pdb=" O LEU J 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'J' and resid 90 through 95 removed outlier: 3.740A pdb=" N VAL J 90 " --> pdb=" O GLN J 43 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU J 42 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU J 51 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 119 through 123 removed outlier: 3.793A pdb=" N VAL J 137 " --> pdb=" O LEU J 184 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 149 through 152 removed outlier: 3.525A pdb=" N ASN J 150 " --> pdb=" O THR J 202 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR J 202 " --> pdb=" O ASN J 150 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS J 152 " --> pdb=" O GLU J 200 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 196 through 198 Processing sheet with id= AY, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.636A pdb=" N VAL K 19 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.668A pdb=" N GLY K 50 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS K 39 " --> pdb=" O ARG K 48 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ARG K 48 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 127 through 130 removed outlier: 3.527A pdb=" N LEU K 148 " --> pdb=" O TYR K 129 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'K' and resid 142 through 144 removed outlier: 3.705A pdb=" N VAL K 143 " --> pdb=" O VAL K 190 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'K' and resid 202 through 206 removed outlier: 4.144A pdb=" N CYS K 202 " --> pdb=" O LYS K 215 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS K 215 " --> pdb=" O CYS K 202 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 2961 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: 21.31 Time building geometry restraints manager: 40.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 25288 1.04 - 1.24: 3314 1.24 - 1.44: 8378 1.44 - 1.64: 14923 1.64 - 1.84: 210 Bond restraints: 52113 Sorted by residual: bond pdb=" N VAL E 92 " pdb=" CA VAL E 92 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.10e-02 8.26e+03 8.52e+00 bond pdb=" N ASN E 96 " pdb=" CA ASN E 96 " ideal model delta sigma weight residual 1.462 1.493 -0.032 1.15e-02 7.56e+03 7.57e+00 bond pdb=" N VAL D 36 " pdb=" CA VAL D 36 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.10e-02 8.26e+03 7.36e+00 bond pdb=" N ARG B 149 " pdb=" H ARG B 149 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" N TYR E 153 " pdb=" CA TYR E 153 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.22e-02 6.72e+03 7.17e+00 ... (remaining 52108 not shown) Histogram of bond angle deviations from ideal: 84.12 - 94.13: 9 94.13 - 104.14: 461 104.14 - 114.16: 63863 114.16 - 124.17: 26532 124.17 - 134.18: 3118 Bond angle restraints: 93983 Sorted by residual: angle pdb=" CB LEU I 53 " pdb=" CG LEU I 53 " pdb=" HG LEU I 53 " ideal model delta sigma weight residual 109.00 84.33 24.67 3.00e+00 1.11e-01 6.76e+01 angle pdb=" CB LEU G 53 " pdb=" CG LEU G 53 " pdb=" HG LEU G 53 " ideal model delta sigma weight residual 109.00 84.53 24.47 3.00e+00 1.11e-01 6.65e+01 angle pdb=" CB LEU K 53 " pdb=" CG LEU K 53 " pdb=" HG LEU K 53 " ideal model delta sigma weight residual 109.00 84.60 24.40 3.00e+00 1.11e-01 6.61e+01 angle pdb=" CD1 LEU I 53 " pdb=" CG LEU I 53 " pdb=" HG LEU I 53 " ideal model delta sigma weight residual 108.00 84.12 23.88 3.00e+00 1.11e-01 6.34e+01 angle pdb=" CD2 LEU I 53 " pdb=" CG LEU I 53 " pdb=" HG LEU I 53 " ideal model delta sigma weight residual 108.00 84.19 23.81 3.00e+00 1.11e-01 6.30e+01 ... (remaining 93978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 23530 21.86 - 43.72: 1225 43.72 - 65.57: 223 65.57 - 87.43: 54 87.43 - 109.29: 19 Dihedral angle restraints: 25051 sinusoidal: 13561 harmonic: 11490 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual 93.00 -178.77 -88.23 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 93 " pdb=" CB CYS F 93 " ideal model delta sinusoidal sigma weight residual 93.00 163.20 -70.20 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS E 130 " pdb=" SG CYS E 130 " pdb=" SG CYS E 144 " pdb=" CB CYS E 144 " ideal model delta sinusoidal sigma weight residual 93.00 36.04 56.96 1 1.00e+01 1.00e-02 4.37e+01 ... (remaining 25048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 4220 0.338 - 0.676: 0 0.676 - 1.014: 0 1.014 - 1.352: 0 1.352 - 1.690: 3 Chirality restraints: 4223 Sorted by residual: chirality pdb=" CG LEU K 53 " pdb=" CB LEU K 53 " pdb=" CD1 LEU K 53 " pdb=" CD2 LEU K 53 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.14e+01 chirality pdb=" CG LEU G 53 " pdb=" CB LEU G 53 " pdb=" CD1 LEU G 53 " pdb=" CD2 LEU G 53 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 7.00e+01 chirality pdb=" CG LEU I 53 " pdb=" CB LEU I 53 " pdb=" CD1 LEU I 53 " pdb=" CD2 LEU I 53 " both_signs ideal model delta sigma weight residual False -2.59 -0.94 -1.65 2.00e-01 2.50e+01 6.79e+01 ... (remaining 4220 not shown) Planarity restraints: 7554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 95 " -0.028 2.00e-02 2.50e+03 1.87e-02 1.05e+01 pdb=" CG TYR C 95 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR C 95 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 95 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 95 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 95 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 95 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 95 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR C 95 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR C 95 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR C 95 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR C 95 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 91 " 0.016 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" N VAL E 92 " -0.051 2.00e-02 2.50e+03 pdb=" CA VAL E 92 " 0.013 2.00e-02 2.50e+03 pdb=" H VAL E 92 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 593 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 594 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.039 5.00e-02 4.00e+02 ... (remaining 7551 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 649 2.07 - 2.70: 80916 2.70 - 3.33: 146047 3.33 - 3.97: 193121 3.97 - 4.60: 299922 Nonbonded interactions: 720655 Sorted by model distance: nonbonded pdb=" HE2 LYS F 154 " pdb=" HA2 GLY F 157 " model vdw 1.437 2.440 nonbonded pdb=" O PRO H 125 " pdb="HH21 ARG I 220 " model vdw 1.443 1.850 nonbonded pdb="HH12 ARG G 48 " pdb=" OE1 GLU G 51 " model vdw 1.505 1.850 nonbonded pdb=" HZ2 LYS F 152 " pdb=" HD2 LYS F 154 " model vdw 1.531 2.270 nonbonded pdb=" HZ3 TRP J 101 " pdb=" OE1 GLU K 51 " model vdw 1.544 2.450 ... (remaining 720650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' selection = (chain 'E' and resid 1 through 449) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.790 Extract box with map and model: 8.470 Check model and map are aligned: 0.820 Set scattering table: 0.500 Process input model: 155.000 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 0.040 26794 Z= 0.283 Angle : 0.596 9.961 36521 Z= 0.316 Chirality : 0.064 1.690 4223 Planarity : 0.004 0.071 4527 Dihedral : 14.246 109.291 9922 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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 (0.15), residues: 3214 helix: 2.70 (0.18), residues: 765 sheet: -0.26 (0.17), residues: 995 loop : -0.39 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 151 HIS 0.009 0.001 HIS E 329 PHE 0.021 0.002 PHE B 203 TYR 0.056 0.002 TYR C 95 ARG 0.006 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 4.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 HIS cc_start: 0.7968 (t-170) cc_final: 0.7653 (m-70) REVERT: C 439 TRP cc_start: 0.7299 (m-10) cc_final: 0.6886 (m100) REVERT: D 332 MET cc_start: 0.8150 (ptm) cc_final: 0.7928 (ptm) REVERT: E 239 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7716 (mt-10) REVERT: E 417 ASP cc_start: 0.7463 (t70) cc_final: 0.7201 (t0) REVERT: F 101 TRP cc_start: 0.7561 (m-90) cc_final: 0.7296 (m-10) REVERT: F 180 MET cc_start: 0.5496 (tmm) cc_final: 0.4511 (ptm) REVERT: G 60 ASN cc_start: 0.7693 (m-40) cc_final: 0.7158 (m110) REVERT: G 64 LYS cc_start: 0.7283 (ttpp) cc_final: 0.7074 (tttp) REVERT: G 107 MET cc_start: 0.7922 (mtt) cc_final: 0.7501 (mtt) REVERT: G 142 MET cc_start: 0.0274 (tpp) cc_final: 0.0015 (tpp) REVERT: G 171 HIS cc_start: 0.4537 (m-70) cc_final: 0.4141 (m-70) REVERT: G 206 HIS cc_start: 0.4482 (t-170) cc_final: 0.4189 (t-90) REVERT: H 24 ARG cc_start: 0.6714 (ttm110) cc_final: 0.6404 (ttm-80) REVERT: H 79 LYS cc_start: 0.7097 (mmmm) cc_final: 0.6803 (mttp) REVERT: I 11 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6579 (mp0) REVERT: J 3 LEU cc_start: 0.7944 (mt) cc_final: 0.7476 (tp) REVERT: J 9 LEU cc_start: 0.7323 (mt) cc_final: 0.7116 (tp) REVERT: K 11 GLU cc_start: 0.6690 (mm-30) cc_final: 0.5972 (mm-30) REVERT: K 85 SER cc_start: 0.6998 (t) cc_final: 0.6524 (p) REVERT: K 90 GLU cc_start: 0.4932 (tp30) cc_final: 0.4650 (tp30) REVERT: K 142 MET cc_start: 0.2771 (tpp) cc_final: 0.2348 (mmt) REVERT: K 213 VAL cc_start: 0.3175 (p) cc_final: 0.2849 (t) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 2.9832 time to fit residues: 1345.8512 Evaluate side-chains 303 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 chunk 151 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 288 optimal weight: 10.0000 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN I 4 GLN I 6 GLN J 35 ASN K 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26794 Z= 0.214 Angle : 0.539 10.361 36521 Z= 0.280 Chirality : 0.062 1.678 4223 Planarity : 0.004 0.054 4527 Dihedral : 7.420 78.149 3883 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.05 % Allowed : 6.05 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3214 helix: 2.90 (0.18), residues: 773 sheet: -0.21 (0.16), residues: 1001 loop : -0.42 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 168 HIS 0.005 0.001 HIS C 297 PHE 0.015 0.001 PHE H 123 TYR 0.030 0.001 TYR C 95 ARG 0.005 0.000 ARG E 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 305 time to evaluate : 4.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 TYR cc_start: 0.8032 (t80) cc_final: 0.7799 (t80) REVERT: B 46 HIS cc_start: 0.8052 (t-170) cc_final: 0.7738 (m-70) REVERT: B 131 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7659 (mmtm) REVERT: C 439 TRP cc_start: 0.7310 (m-10) cc_final: 0.6884 (m100) REVERT: D 332 MET cc_start: 0.8141 (ptm) cc_final: 0.7839 (ptm) REVERT: E 239 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7687 (mt-10) REVERT: E 249 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8202 (tp) REVERT: F 47 GLN cc_start: 0.6227 (mt0) cc_final: 0.5867 (mt0) REVERT: F 66 ARG cc_start: 0.5588 (ptt-90) cc_final: 0.5091 (ptp-170) REVERT: F 84 GLU cc_start: 0.6195 (mp0) cc_final: 0.5752 (mp0) REVERT: G 60 ASN cc_start: 0.7516 (m-40) cc_final: 0.7152 (m110) REVERT: G 107 MET cc_start: 0.7927 (mtt) cc_final: 0.7506 (mtt) REVERT: G 142 MET cc_start: 0.0304 (tpp) cc_final: -0.0095 (tpp) REVERT: G 171 HIS cc_start: 0.4530 (m-70) cc_final: 0.4151 (m-70) REVERT: G 206 HIS cc_start: 0.4113 (t-170) cc_final: 0.3837 (t-90) REVERT: H 1 ASP cc_start: 0.6467 (m-30) cc_final: 0.6222 (m-30) REVERT: H 24 ARG cc_start: 0.6683 (ttm110) cc_final: 0.6461 (ttp-170) REVERT: H 79 LYS cc_start: 0.7070 (mmmm) cc_final: 0.6768 (mttp) REVERT: H 84 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: I 90 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6033 (mt-10) REVERT: J 3 LEU cc_start: 0.7943 (mt) cc_final: 0.7200 (tt) REVERT: K 85 SER cc_start: 0.7001 (t) cc_final: 0.6533 (p) REVERT: K 90 GLU cc_start: 0.4947 (tp30) cc_final: 0.4645 (tp30) REVERT: K 122 LYS cc_start: 0.6004 (mmmm) cc_final: 0.5802 (mtpp) REVERT: K 142 MET cc_start: 0.2757 (tpp) cc_final: 0.2474 (mmt) outliers start: 31 outliers final: 15 residues processed: 327 average time/residue: 2.7836 time to fit residues: 1066.8439 Evaluate side-chains 297 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 279 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 90 GLU Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 93 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 240 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 289 optimal weight: 9.9990 chunk 312 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS F 43 GLN G 40 GLN I 6 GLN K 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26794 Z= 0.216 Angle : 0.527 10.157 36521 Z= 0.270 Chirality : 0.061 1.696 4223 Planarity : 0.004 0.051 4527 Dihedral : 6.175 57.908 3883 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.36 % Allowed : 7.68 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.61 (0.15), residues: 3214 helix: 2.76 (0.18), residues: 791 sheet: -0.13 (0.16), residues: 1033 loop : -0.52 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 161 HIS 0.005 0.001 HIS C 297 PHE 0.013 0.001 PHE I 153 TYR 0.019 0.001 TYR C 95 ARG 0.004 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 278 time to evaluate : 4.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 HIS cc_start: 0.8038 (t-170) cc_final: 0.7705 (m-70) REVERT: B 216 LEU cc_start: 0.8772 (tp) cc_final: 0.8501 (tt) REVERT: C 16 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6973 (ppt170) REVERT: C 228 ILE cc_start: 0.8987 (pt) cc_final: 0.8780 (pp) REVERT: C 439 TRP cc_start: 0.7335 (m-10) cc_final: 0.6896 (m100) REVERT: D 104 ASP cc_start: 0.6963 (t0) cc_final: 0.6600 (t0) REVERT: D 332 MET cc_start: 0.8120 (ptm) cc_final: 0.7887 (ptm) REVERT: E 239 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7700 (mt-10) REVERT: E 249 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8321 (tp) REVERT: F 66 ARG cc_start: 0.5602 (ptt-90) cc_final: 0.5066 (ptp-170) REVERT: F 84 GLU cc_start: 0.6337 (mp0) cc_final: 0.5823 (mp0) REVERT: F 88 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6912 (mm) REVERT: G 60 ASN cc_start: 0.7575 (m-40) cc_final: 0.7301 (m110) REVERT: G 142 MET cc_start: 0.0379 (tpp) cc_final: -0.0091 (tpp) REVERT: G 171 HIS cc_start: 0.4552 (m-70) cc_final: 0.4180 (m-70) REVERT: G 206 HIS cc_start: 0.4128 (t-170) cc_final: 0.3803 (t-90) REVERT: H 1 ASP cc_start: 0.6461 (m-30) cc_final: 0.6194 (m-30) REVERT: H 24 ARG cc_start: 0.6694 (ttm110) cc_final: 0.6403 (ttm-80) REVERT: H 50 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7717 (mptt) REVERT: H 84 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6075 (mm-30) REVERT: I 90 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.6041 (mt-10) REVERT: J 3 LEU cc_start: 0.8012 (mt) cc_final: 0.7295 (tt) REVERT: K 85 SER cc_start: 0.6953 (t) cc_final: 0.6497 (p) REVERT: K 90 GLU cc_start: 0.5047 (tp30) cc_final: 0.4744 (tp30) outliers start: 40 outliers final: 15 residues processed: 302 average time/residue: 2.7626 time to fit residues: 986.3708 Evaluate side-chains 280 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 4.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 90 GLU Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 93 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 290 optimal weight: 0.5980 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 275 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN J 35 ASN K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26794 Z= 0.152 Angle : 0.491 10.262 36521 Z= 0.250 Chirality : 0.061 1.699 4223 Planarity : 0.004 0.051 4527 Dihedral : 5.117 40.782 3883 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.16 % Allowed : 9.01 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.76 (0.15), residues: 3214 helix: 2.97 (0.18), residues: 791 sheet: -0.04 (0.16), residues: 1033 loop : -0.48 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 101 HIS 0.004 0.001 HIS C 297 PHE 0.015 0.001 PHE I 153 TYR 0.011 0.001 TYR J 145 ARG 0.004 0.000 ARG D 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 271 time to evaluate : 4.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7957 (m-80) cc_final: 0.7574 (m-10) REVERT: B 46 HIS cc_start: 0.7971 (t-170) cc_final: 0.7701 (m-70) REVERT: B 131 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7447 (mmtm) REVERT: C 16 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6943 (ppt170) REVERT: C 439 TRP cc_start: 0.7293 (m-10) cc_final: 0.6913 (m100) REVERT: D 104 ASP cc_start: 0.6902 (t0) cc_final: 0.6563 (t0) REVERT: D 332 MET cc_start: 0.8142 (ptm) cc_final: 0.7814 (ptm) REVERT: E 239 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7675 (mt-10) REVERT: E 249 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8229 (tp) REVERT: F 66 ARG cc_start: 0.5612 (ptt-90) cc_final: 0.5086 (ptp-170) REVERT: F 84 GLU cc_start: 0.6166 (mp0) cc_final: 0.5737 (mp0) REVERT: F 88 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6453 (tm) REVERT: G 142 MET cc_start: 0.0369 (tpp) cc_final: -0.0139 (tpp) REVERT: G 171 HIS cc_start: 0.4543 (m-70) cc_final: 0.4176 (m-70) REVERT: G 206 HIS cc_start: 0.4104 (t-170) cc_final: 0.3788 (t-90) REVERT: H 1 ASP cc_start: 0.6438 (m-30) cc_final: 0.6171 (m-30) REVERT: H 24 ARG cc_start: 0.6674 (ttm110) cc_final: 0.6398 (ttm-80) REVERT: H 50 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7708 (mptt) REVERT: H 84 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6089 (mm-30) REVERT: J 3 LEU cc_start: 0.8080 (mt) cc_final: 0.7348 (tt) REVERT: J 24 ARG cc_start: 0.7067 (mtm-85) cc_final: 0.6705 (mtm110) REVERT: K 85 SER cc_start: 0.6986 (t) cc_final: 0.6523 (p) REVERT: K 90 GLU cc_start: 0.4959 (tp30) cc_final: 0.4643 (tp30) outliers start: 34 outliers final: 20 residues processed: 292 average time/residue: 2.7334 time to fit residues: 949.0824 Evaluate side-chains 287 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 262 time to evaluate : 4.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 93 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 156 optimal weight: 0.5980 chunk 275 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 326 GLN I 6 GLN K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26794 Z= 0.192 Angle : 0.505 10.288 36521 Z= 0.259 Chirality : 0.061 1.684 4223 Planarity : 0.004 0.052 4527 Dihedral : 4.798 42.419 3883 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.29 % Allowed : 9.62 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.75 (0.15), residues: 3214 helix: 2.92 (0.18), residues: 791 sheet: 0.01 (0.16), residues: 1003 loop : -0.51 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 101 HIS 0.004 0.001 HIS C 297 PHE 0.015 0.001 PHE I 153 TYR 0.011 0.001 TYR F 37 ARG 0.005 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 272 time to evaluate : 3.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7964 (m-80) cc_final: 0.7570 (m-10) REVERT: B 46 HIS cc_start: 0.7959 (t-170) cc_final: 0.7693 (m-70) REVERT: B 131 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7608 (mmtm) REVERT: B 216 LEU cc_start: 0.8811 (tp) cc_final: 0.8532 (tt) REVERT: B 318 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8374 (mt) REVERT: C 16 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6998 (ppt170) REVERT: C 439 TRP cc_start: 0.7322 (m-10) cc_final: 0.6917 (m100) REVERT: D 104 ASP cc_start: 0.6997 (t0) cc_final: 0.6665 (t0) REVERT: D 332 MET cc_start: 0.8142 (ptm) cc_final: 0.7788 (ptm) REVERT: E 239 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7709 (mt-10) REVERT: E 249 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8297 (tp) REVERT: F 88 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6516 (tm) REVERT: G 142 MET cc_start: 0.0383 (tpp) cc_final: -0.0091 (tpp) REVERT: G 171 HIS cc_start: 0.4547 (m-70) cc_final: 0.4145 (m-70) REVERT: G 206 HIS cc_start: 0.4063 (t-170) cc_final: 0.3750 (t-90) REVERT: H 1 ASP cc_start: 0.6310 (m-30) cc_final: 0.6037 (m-30) REVERT: H 24 ARG cc_start: 0.6648 (ttm110) cc_final: 0.6385 (ttm-80) REVERT: H 50 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7720 (mptt) REVERT: H 84 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.6180 (mm-30) REVERT: I 47 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7673 (mt-10) REVERT: J 3 LEU cc_start: 0.8178 (mt) cc_final: 0.7367 (tt) REVERT: J 24 ARG cc_start: 0.7090 (mtm-85) cc_final: 0.6736 (mtm110) REVERT: K 85 SER cc_start: 0.6961 (t) cc_final: 0.6507 (p) REVERT: K 90 GLU cc_start: 0.5116 (tp30) cc_final: 0.4801 (tp30) outliers start: 38 outliers final: 22 residues processed: 295 average time/residue: 2.6847 time to fit residues: 935.9337 Evaluate side-chains 295 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 267 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 107 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.7980 chunk 276 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 326 GLN I 6 GLN K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26794 Z= 0.174 Angle : 0.496 10.354 36521 Z= 0.253 Chirality : 0.061 1.693 4223 Planarity : 0.004 0.051 4527 Dihedral : 4.593 42.512 3883 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.39 % Allowed : 10.00 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3214 helix: 2.97 (0.18), residues: 791 sheet: 0.07 (0.16), residues: 1003 loop : -0.51 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 101 HIS 0.004 0.001 HIS C 297 PHE 0.017 0.001 PHE I 153 TYR 0.011 0.001 TYR C 428 ARG 0.012 0.000 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 270 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7976 (m-80) cc_final: 0.7583 (m-10) REVERT: B 46 HIS cc_start: 0.7948 (t-170) cc_final: 0.7688 (m-70) REVERT: B 131 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7643 (mmtm) REVERT: B 216 LEU cc_start: 0.8808 (tp) cc_final: 0.8520 (tt) REVERT: B 318 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8401 (mt) REVERT: C 16 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6954 (ppt170) REVERT: C 439 TRP cc_start: 0.7329 (m-10) cc_final: 0.6905 (m100) REVERT: D 104 ASP cc_start: 0.7015 (t0) cc_final: 0.6731 (t0) REVERT: D 332 MET cc_start: 0.8146 (ptm) cc_final: 0.7891 (ptm) REVERT: D 578 TRP cc_start: 0.7608 (m-10) cc_final: 0.7048 (m100) REVERT: E 239 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7708 (mt-10) REVERT: E 249 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8216 (tp) REVERT: F 88 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6525 (tm) REVERT: G 142 MET cc_start: 0.0575 (tpp) cc_final: 0.0115 (tpp) REVERT: G 171 HIS cc_start: 0.4503 (m-70) cc_final: 0.4109 (m-70) REVERT: H 1 ASP cc_start: 0.6297 (m-30) cc_final: 0.6009 (m-30) REVERT: H 50 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7647 (mptt) REVERT: H 84 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6176 (mm-30) REVERT: H 108 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6315 (tptt) REVERT: I 47 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7647 (mt-10) REVERT: J 3 LEU cc_start: 0.8185 (mt) cc_final: 0.7384 (tt) REVERT: J 24 ARG cc_start: 0.7119 (mtm-85) cc_final: 0.6778 (mtm110) REVERT: K 85 SER cc_start: 0.7118 (t) cc_final: 0.6623 (p) REVERT: K 90 GLU cc_start: 0.5093 (tp30) cc_final: 0.4767 (tp30) outliers start: 41 outliers final: 22 residues processed: 296 average time/residue: 2.6943 time to fit residues: 946.1775 Evaluate side-chains 294 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 265 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain J residue 93 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 0.1980 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 326 GLN E 50 GLN I 6 GLN K 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26794 Z= 0.258 Angle : 0.544 10.279 36521 Z= 0.281 Chirality : 0.061 1.666 4223 Planarity : 0.005 0.054 4527 Dihedral : 4.887 48.081 3883 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.50 % Allowed : 10.51 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.59 (0.15), residues: 3214 helix: 2.73 (0.18), residues: 791 sheet: -0.01 (0.16), residues: 1003 loop : -0.61 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 596 HIS 0.005 0.001 HIS C 297 PHE 0.018 0.002 PHE I 153 TYR 0.016 0.002 TYR F 37 ARG 0.005 0.001 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 264 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 HIS cc_start: 0.7878 (t-170) cc_final: 0.7641 (m-70) REVERT: B 131 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7707 (mmtm) REVERT: B 216 LEU cc_start: 0.8791 (tp) cc_final: 0.8531 (tt) REVERT: B 318 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8495 (mt) REVERT: C 16 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7125 (ppt170) REVERT: C 268 ASP cc_start: 0.7671 (t0) cc_final: 0.7413 (m-30) REVERT: D 332 MET cc_start: 0.8139 (ptm) cc_final: 0.7878 (ptm) REVERT: E 239 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7746 (mt-10) REVERT: E 249 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8291 (tp) REVERT: F 88 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6529 (tm) REVERT: G 142 MET cc_start: 0.0593 (tpp) cc_final: 0.0149 (tpp) REVERT: G 171 HIS cc_start: 0.4492 (m-70) cc_final: 0.4117 (m-70) REVERT: G 206 HIS cc_start: 0.3920 (t-170) cc_final: 0.3423 (t-90) REVERT: H 1 ASP cc_start: 0.6515 (m-30) cc_final: 0.6189 (m-30) REVERT: H 44 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7436 (mttm) REVERT: H 84 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6177 (mm-30) REVERT: I 47 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7710 (mt-10) REVERT: J 3 LEU cc_start: 0.8170 (mt) cc_final: 0.7300 (tt) REVERT: J 24 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6758 (mtm110) REVERT: J 195 ASN cc_start: 0.5210 (m-40) cc_final: 0.4747 (p0) REVERT: K 85 SER cc_start: 0.7130 (t) cc_final: 0.6631 (p) REVERT: K 90 GLU cc_start: 0.5148 (tp30) cc_final: 0.4864 (tp30) outliers start: 44 outliers final: 24 residues processed: 293 average time/residue: 2.6472 time to fit residues: 916.8276 Evaluate side-chains 282 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 253 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 171 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 183 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 326 GLN I 6 GLN K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26794 Z= 0.200 Angle : 0.513 10.475 36521 Z= 0.264 Chirality : 0.061 1.693 4223 Planarity : 0.004 0.051 4527 Dihedral : 4.777 47.303 3883 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.09 % Allowed : 11.15 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.15), residues: 3214 helix: 2.83 (0.18), residues: 791 sheet: 0.00 (0.16), residues: 1003 loop : -0.60 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 101 HIS 0.005 0.001 HIS C 297 PHE 0.018 0.001 PHE I 153 TYR 0.014 0.001 TYR G 105 ARG 0.003 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 258 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 HIS cc_start: 0.7871 (t-170) cc_final: 0.7636 (m-70) REVERT: B 131 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7677 (mmtm) REVERT: B 216 LEU cc_start: 0.8772 (tp) cc_final: 0.8508 (tt) REVERT: B 318 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8482 (mt) REVERT: C 268 ASP cc_start: 0.7677 (t0) cc_final: 0.7423 (m-30) REVERT: D 332 MET cc_start: 0.8091 (ptm) cc_final: 0.7825 (ptm) REVERT: D 578 TRP cc_start: 0.7623 (m-10) cc_final: 0.7078 (m100) REVERT: E 239 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7739 (mt-10) REVERT: E 249 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8283 (tp) REVERT: F 88 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6510 (tm) REVERT: G 142 MET cc_start: 0.0658 (tpp) cc_final: 0.0264 (tpp) REVERT: G 171 HIS cc_start: 0.4474 (m-70) cc_final: 0.4110 (m-70) REVERT: H 1 ASP cc_start: 0.6404 (m-30) cc_final: 0.6129 (m-30) REVERT: H 44 LYS cc_start: 0.7668 (mtpt) cc_final: 0.7417 (mttm) REVERT: H 50 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7568 (mptt) REVERT: H 84 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6231 (mm-30) REVERT: I 47 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7697 (mt-10) REVERT: J 3 LEU cc_start: 0.8192 (mt) cc_final: 0.7321 (tt) REVERT: J 9 LEU cc_start: 0.7064 (tp) cc_final: 0.6592 (mm) REVERT: J 24 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.6736 (mtm110) REVERT: J 195 ASN cc_start: 0.5606 (m-40) cc_final: 0.4836 (p0) REVERT: K 85 SER cc_start: 0.7115 (t) cc_final: 0.6613 (p) REVERT: K 90 GLU cc_start: 0.5098 (tp30) cc_final: 0.4809 (tp30) outliers start: 32 outliers final: 20 residues processed: 280 average time/residue: 2.7638 time to fit residues: 917.8051 Evaluate side-chains 282 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 257 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain J residue 93 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.9990 chunk 293 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 284 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN J 58 ASN K 60 ASN K 203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 26794 Z= 0.298 Angle : 0.560 10.373 36521 Z= 0.291 Chirality : 0.062 1.668 4223 Planarity : 0.005 0.054 4527 Dihedral : 5.112 53.551 3883 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.36 % Allowed : 11.32 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.47 (0.15), residues: 3214 helix: 2.63 (0.18), residues: 788 sheet: -0.06 (0.16), residues: 1003 loop : -0.71 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 101 HIS 0.006 0.001 HIS C 297 PHE 0.017 0.002 PHE A 262 TYR 0.031 0.002 TYR G 105 ARG 0.006 0.001 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 261 time to evaluate : 4.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 HIS cc_start: 0.7881 (t-170) cc_final: 0.7647 (m-70) REVERT: B 131 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7721 (mmtm) REVERT: B 216 LEU cc_start: 0.8799 (tp) cc_final: 0.8549 (tt) REVERT: B 318 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8508 (mt) REVERT: C 268 ASP cc_start: 0.7593 (t0) cc_final: 0.7385 (m-30) REVERT: C 324 MET cc_start: 0.7714 (mtp) cc_final: 0.7466 (mtp) REVERT: D 332 MET cc_start: 0.8045 (ptm) cc_final: 0.7768 (ptm) REVERT: D 578 TRP cc_start: 0.7642 (m-10) cc_final: 0.7089 (m100) REVERT: E 239 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7767 (mt-10) REVERT: E 249 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8313 (tp) REVERT: F 88 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6486 (tm) REVERT: G 142 MET cc_start: 0.0374 (tpp) cc_final: 0.0065 (tpp) REVERT: H 1 ASP cc_start: 0.6551 (m-30) cc_final: 0.6262 (m-30) REVERT: H 44 LYS cc_start: 0.7653 (mtpt) cc_final: 0.7364 (mttm) REVERT: H 50 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7576 (mptt) REVERT: H 84 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6222 (mm-30) REVERT: I 11 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6577 (mm-30) REVERT: I 47 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7711 (mt-10) REVERT: I 105 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7439 (p90) REVERT: J 3 LEU cc_start: 0.8182 (mt) cc_final: 0.7310 (tt) REVERT: J 9 LEU cc_start: 0.7062 (tp) cc_final: 0.6594 (mm) REVERT: J 24 ARG cc_start: 0.6926 (mtm-85) cc_final: 0.6717 (mtm110) REVERT: J 108 LYS cc_start: 0.7616 (tppp) cc_final: 0.7368 (tppt) REVERT: J 195 ASN cc_start: 0.5657 (m-40) cc_final: 0.4832 (p0) REVERT: K 85 SER cc_start: 0.7125 (t) cc_final: 0.6592 (p) REVERT: K 90 GLU cc_start: 0.5044 (tp30) cc_final: 0.4748 (tp30) REVERT: K 112 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7625 (pt0) outliers start: 40 outliers final: 25 residues processed: 290 average time/residue: 2.7524 time to fit residues: 936.8177 Evaluate side-chains 288 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 256 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 8.9990 chunk 302 optimal weight: 0.0070 chunk 184 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 316 optimal weight: 0.7980 chunk 291 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN J 27 GLN K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26794 Z= 0.180 Angle : 0.506 10.545 36521 Z= 0.260 Chirality : 0.061 1.695 4223 Planarity : 0.004 0.051 4527 Dihedral : 4.801 50.146 3883 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 0.95 % Allowed : 11.87 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3214 helix: 2.83 (0.18), residues: 791 sheet: -0.02 (0.16), residues: 1009 loop : -0.61 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 101 HIS 0.004 0.001 HIS C 298 PHE 0.017 0.001 PHE I 153 TYR 0.016 0.001 TYR G 105 ARG 0.002 0.000 ARG J 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 263 time to evaluate : 4.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 HIS cc_start: 0.7868 (t-170) cc_final: 0.7638 (m-70) REVERT: B 131 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7683 (mmtm) REVERT: B 216 LEU cc_start: 0.8764 (tp) cc_final: 0.8509 (tt) REVERT: B 318 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8497 (mt) REVERT: C 268 ASP cc_start: 0.7672 (t0) cc_final: 0.7442 (m-30) REVERT: D 104 ASP cc_start: 0.6953 (t0) cc_final: 0.6657 (t0) REVERT: D 332 MET cc_start: 0.8074 (ptm) cc_final: 0.7805 (ptm) REVERT: D 578 TRP cc_start: 0.7609 (m-10) cc_final: 0.7070 (m100) REVERT: E 239 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7741 (mt-10) REVERT: E 249 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8278 (tp) REVERT: F 88 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6475 (tm) REVERT: G 142 MET cc_start: 0.0828 (tpp) cc_final: 0.0436 (tpp) REVERT: G 206 HIS cc_start: 0.3961 (t-170) cc_final: 0.3713 (t-170) REVERT: H 1 ASP cc_start: 0.6434 (m-30) cc_final: 0.6176 (m-30) REVERT: H 50 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7566 (mptt) REVERT: H 84 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6352 (mm-30) REVERT: I 11 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6602 (mt-10) REVERT: I 47 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7705 (mt-10) REVERT: I 105 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.7365 (p90) REVERT: J 3 LEU cc_start: 0.8179 (mt) cc_final: 0.7310 (tt) REVERT: J 9 LEU cc_start: 0.7048 (tp) cc_final: 0.6598 (mm) REVERT: J 79 LYS cc_start: 0.7329 (mttp) cc_final: 0.7078 (mttp) REVERT: J 108 LYS cc_start: 0.7605 (tppp) cc_final: 0.7360 (tppt) REVERT: J 195 ASN cc_start: 0.5518 (m-40) cc_final: 0.4840 (p0) REVERT: K 85 SER cc_start: 0.6810 (t) cc_final: 0.6353 (p) REVERT: K 90 GLU cc_start: 0.5029 (tp30) cc_final: 0.4741 (tp30) outliers start: 28 outliers final: 19 residues processed: 283 average time/residue: 2.6972 time to fit residues: 907.1681 Evaluate side-chains 285 residues out of total 2941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 260 time to evaluate : 3.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain K residue 105 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 7.9990 chunk 268 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN K 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097039 restraints weight = 89173.665| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.67 r_work: 0.2958 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26794 Z= 0.291 Angle : 0.559 10.389 36521 Z= 0.290 Chirality : 0.062 1.670 4223 Planarity : 0.005 0.054 4527 Dihedral : 5.137 53.395 3883 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 1.09 % Allowed : 11.97 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.46 (0.15), residues: 3214 helix: 2.62 (0.18), residues: 788 sheet: -0.09 (0.16), residues: 1009 loop : -0.70 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 101 HIS 0.006 0.001 HIS C 297 PHE 0.018 0.002 PHE A 262 TYR 0.031 0.002 TYR G 105 ARG 0.006 0.001 ARG D 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17087.35 seconds wall clock time: 300 minutes 23.69 seconds (18023.69 seconds total)