Starting phenix.real_space_refine on Sun Aug 4 14:11:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt2_43516/08_2024/8vt2_43516.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt2_43516/08_2024/8vt2_43516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt2_43516/08_2024/8vt2_43516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt2_43516/08_2024/8vt2_43516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt2_43516/08_2024/8vt2_43516.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt2_43516/08_2024/8vt2_43516.cif" } resolution = 3.14 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= 0.001 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6678 2.51 5 N 1818 2.21 5 O 2115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B ASP 331": "OD1" <-> "OD2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10674 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3477 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain breaks: 1 Chain: "B" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3477 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain breaks: 1 Chain: "C" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3477 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.25, per 1000 atoms: 0.59 Number of scatterers: 10674 At special positions: 0 Unit cell: (83.424, 87.216, 133.668, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2115 8.00 N 1818 7.00 C 6678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 501 " - " ASN A 353 " " NAG B 501 " - " ASN B 353 " " NAG D 1 " - " ASN A 172 " " NAG E 1 " - " ASN A 57 " " NAG F 1 " - " ASN B 172 " " NAG G 1 " - " ASN B 57 " " NAG H 1 " - " ASN C 172 " " NAG I 1 " - " ASN C 57 " Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 2.0 seconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 36.7% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.653A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.734A pdb=" N ALA A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 129 removed outlier: 3.846A pdb=" N THR A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 163 through 172 removed outlier: 3.558A pdb=" N ASP A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.521A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.638A pdb=" N ASN A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.720A pdb=" N CYS A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.899A pdb=" N GLY A 340 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.871A pdb=" N LYS A 348 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 460 through 480 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.653A pdb=" N THR B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 removed outlier: 3.836A pdb=" N ALA B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.840A pdb=" N THR B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.645A pdb=" N ASP B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.536A pdb=" N ALA B 176 " --> pdb=" O ASN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 removed outlier: 3.535A pdb=" N VAL B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 210 removed outlier: 3.639A pdb=" N ASN B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 344 through 350 removed outlier: 3.885A pdb=" N LYS B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS B 350 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 480 Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 66 through 81 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.916A pdb=" N ALA C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.663A pdb=" N ALA C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 197 through 210 removed outlier: 3.676A pdb=" N ASN C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 344 through 350 removed outlier: 3.898A pdb=" N CYS C 350 " --> pdb=" O SER C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.766A pdb=" N PHE C 446 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 480 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 24 removed outlier: 7.138A pdb=" N SER A 29 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 288 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A 31 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 286 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU A 33 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TRP A 284 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR A 35 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER A 37 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 320 current: chain 'A' and resid 332 through 334 Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 150 removed outlier: 9.421A pdb=" N TRP A 43 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N LEU A 158 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR A 45 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR A 160 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 47 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL A 162 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A 49 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 257 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295 Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 376 Processing sheet with id=AA5, first strand: chain 'A' and resid 399 through 402 Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 24 removed outlier: 7.183A pdb=" N SER B 29 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 288 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 31 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 286 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU B 33 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TRP B 284 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TYR B 35 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER B 37 " --> pdb=" O ASP B 280 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 278 " --> pdb=" O LEU B 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 316 through 320 current: chain 'B' and resid 332 through 336 Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 150 removed outlier: 8.307A pdb=" N ARG B 156 " --> pdb=" O TRP B 43 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N THR B 45 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL B 262 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 257 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 295 Processing sheet with id=AA9, first strand: chain 'B' and resid 372 through 376 Processing sheet with id=AB1, first strand: chain 'B' and resid 399 through 402 Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 29 through 51 current: chain 'C' and resid 156 through 162 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 156 through 162 current: chain 'C' and resid 256 through 263 removed outlier: 6.702A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 316 through 320 current: chain 'C' and resid 332 through 336 Processing sheet with id=AB3, first strand: chain 'C' and resid 291 through 295 removed outlier: 7.522A pdb=" N THR C 365 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE C 456 " --> pdb=" O THR C 365 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 372 through 376 Processing sheet with id=AB5, first strand: chain 'C' and resid 399 through 402 493 hydrogen bonds defined for protein. 1290 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: 3.14 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2943 1.33 - 1.45: 1680 1.45 - 1.57: 6115 1.57 - 1.69: 2 1.69 - 1.81: 84 Bond restraints: 10824 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.59e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" CB THR C 160 " pdb=" CG2 THR C 160 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.29e+00 bond pdb=" CB THR A 160 " pdb=" CG2 THR A 160 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.98e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 ... (remaining 10819 not shown) Histogram of bond angle deviations from ideal: 96.15 - 103.76: 112 103.76 - 111.37: 4802 111.37 - 118.98: 4142 118.98 - 126.59: 5521 126.59 - 134.20: 84 Bond angle restraints: 14661 Sorted by residual: angle pdb=" N ILE A 420 " pdb=" CA ILE A 420 " pdb=" C ILE A 420 " ideal model delta sigma weight residual 109.46 103.74 5.72 1.38e+00 5.25e-01 1.72e+01 angle pdb=" N ILE C 352 " pdb=" CA ILE C 352 " pdb=" C ILE C 352 " ideal model delta sigma weight residual 112.12 109.00 3.12 8.40e-01 1.42e+00 1.38e+01 angle pdb=" N ARG A 248 " pdb=" CA ARG A 248 " pdb=" C ARG A 248 " ideal model delta sigma weight residual 110.80 118.22 -7.42 2.13e+00 2.20e-01 1.21e+01 angle pdb=" N ARG C 248 " pdb=" CA ARG C 248 " pdb=" C ARG C 248 " ideal model delta sigma weight residual 110.80 118.06 -7.26 2.13e+00 2.20e-01 1.16e+01 angle pdb=" C THR C 411 " pdb=" N ASN C 412 " pdb=" CA ASN C 412 " ideal model delta sigma weight residual 122.56 116.85 5.71 1.72e+00 3.38e-01 1.10e+01 ... (remaining 14656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 6360 21.72 - 43.43: 352 43.43 - 65.15: 76 65.15 - 86.86: 29 86.86 - 108.58: 14 Dihedral angle restraints: 6831 sinusoidal: 2886 harmonic: 3945 Sorted by residual: dihedral pdb=" CA ILE A 420 " pdb=" C ILE A 420 " pdb=" N ASP A 421 " pdb=" CA ASP A 421 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ILE B 420 " pdb=" C ILE B 420 " pdb=" N ASP B 421 " pdb=" CA ASP B 421 " ideal model delta harmonic sigma weight residual 180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE C 420 " pdb=" C ILE C 420 " pdb=" N ASP C 421 " pdb=" CA ASP C 421 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 6828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 1753 0.140 - 0.279: 27 0.279 - 0.419: 3 0.419 - 0.558: 0 0.558 - 0.698: 1 Chirality restraints: 1784 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CB THR C 357 " pdb=" CA THR C 357 " pdb=" OG1 THR C 357 " pdb=" CG2 THR C 357 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB THR A 357 " pdb=" CA THR A 357 " pdb=" OG1 THR A 357 " pdb=" CG2 THR A 357 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1781 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 193 " 0.021 2.00e-02 2.50e+03 2.58e-02 1.16e+01 pdb=" CG PHE C 193 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE C 193 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE C 193 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 193 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 193 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 193 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 193 " 0.021 2.00e-02 2.50e+03 2.57e-02 1.15e+01 pdb=" CG PHE A 193 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE A 193 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 193 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 193 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 193 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 193 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 63 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO C 64 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.028 5.00e-02 4.00e+02 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 439 2.70 - 3.25: 9958 3.25 - 3.80: 15146 3.80 - 4.35: 20625 4.35 - 4.90: 36543 Nonbonded interactions: 82711 Sorted by model distance: nonbonded pdb=" OG1 THR C 45 " pdb=" OE1 GLN C 272 " model vdw 2.144 3.040 nonbonded pdb=" O ASP C 62 " pdb=" O6 BMA F 3 " model vdw 2.145 3.040 nonbonded pdb=" OE2 GLU B 305 " pdb=" OG SER B 364 " model vdw 2.149 3.040 nonbonded pdb=" OE2 GLU A 305 " pdb=" OG SER A 364 " model vdw 2.152 3.040 nonbonded pdb=" OG1 THR B 45 " pdb=" OE1 GLN B 272 " model vdw 2.162 3.040 ... (remaining 82706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 0.950 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: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.440 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.014 0.086 10824 Z= 0.876 Angle : 0.957 8.841 14661 Z= 0.511 Chirality : 0.064 0.698 1784 Planarity : 0.006 0.049 1857 Dihedral : 15.923 108.580 4278 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.22), residues: 1350 helix: 0.14 (0.25), residues: 408 sheet: -0.02 (0.28), residues: 345 loop : -2.13 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 473 HIS 0.005 0.002 HIS C 435 PHE 0.059 0.003 PHE C 193 TYR 0.022 0.004 TYR C 310 ARG 0.008 0.001 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: C 54 ASP cc_start: 0.7987 (p0) cc_final: 0.7681 (p0) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3275 time to fit residues: 45.7779 Evaluate side-chains 92 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 402 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10824 Z= 0.180 Angle : 0.621 7.257 14661 Z= 0.319 Chirality : 0.048 0.488 1784 Planarity : 0.005 0.047 1857 Dihedral : 12.257 94.206 1836 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.52 % Allowed : 3.70 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1350 helix: 0.69 (0.25), residues: 429 sheet: 0.16 (0.27), residues: 342 loop : -1.78 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS A 332 PHE 0.019 0.001 PHE A 193 TYR 0.011 0.001 TYR A 385 ARG 0.004 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.154 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 104 average time/residue: 0.2851 time to fit residues: 40.0948 Evaluate side-chains 97 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 132 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 41 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 457 ASN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN C 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10824 Z= 0.152 Angle : 0.564 7.218 14661 Z= 0.287 Chirality : 0.047 0.548 1784 Planarity : 0.004 0.045 1857 Dihedral : 10.025 83.252 1836 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.34 % Allowed : 5.86 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.23), residues: 1350 helix: 1.15 (0.25), residues: 435 sheet: 0.33 (0.28), residues: 345 loop : -1.55 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.001 0.001 HIS A 332 PHE 0.014 0.001 PHE C 193 TYR 0.012 0.001 TYR A 385 ARG 0.005 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.225 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 100 average time/residue: 0.2621 time to fit residues: 36.6565 Evaluate side-chains 89 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN C 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10824 Z= 0.339 Angle : 0.629 7.481 14661 Z= 0.319 Chirality : 0.050 0.539 1784 Planarity : 0.005 0.044 1857 Dihedral : 9.243 77.224 1836 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.69 % Allowed : 7.32 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1350 helix: 1.09 (0.25), residues: 429 sheet: 0.16 (0.27), residues: 345 loop : -1.58 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 284 HIS 0.002 0.001 HIS C 435 PHE 0.025 0.002 PHE C 193 TYR 0.011 0.002 TYR A 319 ARG 0.004 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 1.190 Fit side-chains REVERT: B 197 ASN cc_start: 0.8646 (p0) cc_final: 0.8401 (p0) REVERT: C 197 ASN cc_start: 0.8543 (p0) cc_final: 0.8228 (p0) outliers start: 8 outliers final: 6 residues processed: 103 average time/residue: 0.2745 time to fit residues: 38.4533 Evaluate side-chains 96 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN C 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10824 Z= 0.355 Angle : 0.636 7.815 14661 Z= 0.323 Chirality : 0.050 0.534 1784 Planarity : 0.005 0.043 1857 Dihedral : 8.707 70.774 1836 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.12 % Allowed : 8.96 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.23), residues: 1350 helix: 1.03 (0.25), residues: 429 sheet: 0.02 (0.27), residues: 345 loop : -1.62 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.002 0.001 HIS C 435 PHE 0.023 0.001 PHE C 193 TYR 0.011 0.002 TYR C 310 ARG 0.005 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 1.191 Fit side-chains REVERT: B 197 ASN cc_start: 0.8695 (p0) cc_final: 0.8439 (p0) REVERT: C 197 ASN cc_start: 0.8647 (p0) cc_final: 0.8359 (p0) outliers start: 13 outliers final: 11 residues processed: 105 average time/residue: 0.2545 time to fit residues: 37.0956 Evaluate side-chains 102 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 357 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 0.0030 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 125 optimal weight: 0.0980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN C 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10824 Z= 0.141 Angle : 0.545 8.015 14661 Z= 0.276 Chirality : 0.046 0.448 1784 Planarity : 0.004 0.044 1857 Dihedral : 7.846 59.617 1836 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.95 % Allowed : 9.47 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1350 helix: 1.35 (0.25), residues: 435 sheet: 0.28 (0.28), residues: 345 loop : -1.38 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.001 0.001 HIS C 332 PHE 0.010 0.001 PHE C 193 TYR 0.012 0.001 TYR A 385 ARG 0.006 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.186 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.2686 time to fit residues: 37.2250 Evaluate side-chains 95 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN C 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10824 Z= 0.275 Angle : 0.592 8.192 14661 Z= 0.300 Chirality : 0.048 0.511 1784 Planarity : 0.004 0.044 1857 Dihedral : 7.572 59.239 1836 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.03 % Allowed : 10.08 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1350 helix: 1.32 (0.26), residues: 432 sheet: 0.20 (0.27), residues: 345 loop : -1.43 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.002 0.001 HIS C 332 PHE 0.016 0.001 PHE C 193 TYR 0.010 0.002 TYR B 310 ARG 0.006 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.172 Fit side-chains REVERT: B 197 ASN cc_start: 0.8584 (p0) cc_final: 0.8322 (p0) REVERT: C 197 ASN cc_start: 0.8523 (p0) cc_final: 0.8235 (p0) outliers start: 12 outliers final: 10 residues processed: 101 average time/residue: 0.2749 time to fit residues: 38.1868 Evaluate side-chains 99 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN C 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10824 Z= 0.144 Angle : 0.542 8.025 14661 Z= 0.275 Chirality : 0.046 0.505 1784 Planarity : 0.004 0.044 1857 Dihedral : 6.974 57.777 1836 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.95 % Allowed : 10.34 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1350 helix: 1.43 (0.25), residues: 438 sheet: 0.39 (0.28), residues: 345 loop : -1.36 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.001 0.001 HIS C 332 PHE 0.009 0.001 PHE C 193 TYR 0.011 0.001 TYR A 385 ARG 0.009 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.167 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.2606 time to fit residues: 36.2493 Evaluate side-chains 98 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.0870 chunk 79 optimal weight: 0.3980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10824 Z= 0.172 Angle : 0.541 7.654 14661 Z= 0.274 Chirality : 0.046 0.510 1784 Planarity : 0.004 0.044 1857 Dihedral : 6.609 58.100 1836 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.86 % Allowed : 10.51 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1350 helix: 1.51 (0.25), residues: 438 sheet: 0.37 (0.28), residues: 345 loop : -1.30 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.001 0.001 HIS C 332 PHE 0.011 0.001 PHE C 193 TYR 0.010 0.001 TYR A 385 ARG 0.007 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.193 Fit side-chains REVERT: B 197 ASN cc_start: 0.8439 (p0) cc_final: 0.8183 (p0) outliers start: 10 outliers final: 10 residues processed: 99 average time/residue: 0.2661 time to fit residues: 36.6190 Evaluate side-chains 99 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 65 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10824 Z= 0.242 Angle : 0.572 7.130 14661 Z= 0.291 Chirality : 0.047 0.504 1784 Planarity : 0.004 0.044 1857 Dihedral : 6.430 59.277 1836 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.86 % Allowed : 10.77 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1350 helix: 1.44 (0.25), residues: 435 sheet: 0.31 (0.27), residues: 345 loop : -1.34 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS C 332 PHE 0.014 0.001 PHE C 193 TYR 0.010 0.001 TYR A 269 ARG 0.007 0.000 ARG C 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: B 197 ASN cc_start: 0.8532 (p0) cc_final: 0.8245 (p0) REVERT: C 197 ASN cc_start: 0.8480 (p0) cc_final: 0.8203 (p0) outliers start: 10 outliers final: 10 residues processed: 99 average time/residue: 0.2700 time to fit residues: 36.7891 Evaluate side-chains 98 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 0.0670 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.096555 restraints weight = 11541.553| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.43 r_work: 0.2920 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10824 Z= 0.230 Angle : 0.564 7.126 14661 Z= 0.288 Chirality : 0.047 0.501 1784 Planarity : 0.004 0.044 1857 Dihedral : 6.231 59.090 1836 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.03 % Allowed : 10.59 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1350 helix: 1.48 (0.25), residues: 435 sheet: 0.31 (0.27), residues: 345 loop : -1.33 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.002 0.001 HIS C 332 PHE 0.013 0.001 PHE C 193 TYR 0.010 0.001 TYR A 385 ARG 0.007 0.000 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2126.67 seconds wall clock time: 38 minutes 50.56 seconds (2330.56 seconds total)