Starting phenix.real_space_refine on Sun Mar 17 12:20:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wej_21649/03_2024/6wej_21649_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wej_21649/03_2024/6wej_21649.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wej_21649/03_2024/6wej_21649_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wej_21649/03_2024/6wej_21649_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wej_21649/03_2024/6wej_21649_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wej_21649/03_2024/6wej_21649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wej_21649/03_2024/6wej_21649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wej_21649/03_2024/6wej_21649_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wej_21649/03_2024/6wej_21649_neut_updated.pdb" } resolution = 2.6 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= 0.139 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 96 5.16 5 Na 1 4.78 5 C 11580 2.51 5 N 2864 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 106": "NH1" <-> "NH2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 600": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B ARG 421": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "B ARG 574": "NH1" <-> "NH2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B ARG 600": "NH1" <-> "NH2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 421": "NH1" <-> "NH2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C ARG 600": "NH1" <-> "NH2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D ARG 421": "NH1" <-> "NH2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D GLU 504": "OE1" <-> "OE2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D GLU 560": "OE1" <-> "OE2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D ARG 600": "NH1" <-> "NH2" Residue "D ARG 614": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17665 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4241 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 15, 'TRANS': 497} Chain breaks: 1 Chain: "B" Number of atoms: 4241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4241 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 15, 'TRANS': 497} Chain breaks: 1 Chain: "C" Number of atoms: 4241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4241 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 15, 'TRANS': 497} Chain breaks: 1 Chain: "D" Number of atoms: 4241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4241 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 15, 'TRANS': 497} Chain breaks: 1 Chain: "A" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 176 Unusual residues: {' NA': 1, 'CPL': 6, 'PX2': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 5, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Unusual residues: {'CPL': 6, 'PX2': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 5, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Unusual residues: {'CPL': 6, 'PX2': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 5, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Unusual residues: {'CPL': 6, 'PX2': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 5, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 9.28, per 1000 atoms: 0.53 Number of scatterers: 17665 At special positions: 0 Unit cell: (120.91, 120.91, 139.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 16 15.00 Na 1 11.00 O 3108 8.00 N 2864 7.00 C 11580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 172 " 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 Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 3.1 seconds 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 12 sheets defined 54.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 120 through 144 Processing helix chain 'A' and resid 194 through 223 removed outlier: 6.596A pdb=" N HIS A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 249 through 257 removed outlier: 4.064A pdb=" N LEU A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 277 through 285 removed outlier: 4.446A pdb=" N ASN A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 304 through 334 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 386 through 417 Processing helix chain 'A' and resid 419 through 437 Processing helix chain 'A' and resid 442 through 456 Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 473 through 488 removed outlier: 5.462A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 592 through 600 Processing helix chain 'A' and resid 603 through 618 Processing helix chain 'B' and resid 105 through 111 Processing helix chain 'B' and resid 120 through 144 Processing helix chain 'B' and resid 194 through 223 removed outlier: 6.596A pdb=" N HIS B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 Processing helix chain 'B' and resid 249 through 257 removed outlier: 4.078A pdb=" N LEU B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 262 Processing helix chain 'B' and resid 277 through 285 removed outlier: 4.446A pdb=" N ASN B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 Processing helix chain 'B' and resid 304 through 334 Processing helix chain 'B' and resid 359 through 374 Processing helix chain 'B' and resid 386 through 417 Processing helix chain 'B' and resid 419 through 437 Processing helix chain 'B' and resid 442 through 456 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 473 through 488 removed outlier: 5.461A pdb=" N GLU B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N THR B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 592 through 600 Processing helix chain 'B' and resid 603 through 618 Processing helix chain 'C' and resid 105 through 111 Processing helix chain 'C' and resid 120 through 144 Processing helix chain 'C' and resid 194 through 223 removed outlier: 6.596A pdb=" N HIS C 199 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 249 through 257 removed outlier: 4.079A pdb=" N LEU C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 262 Processing helix chain 'C' and resid 277 through 285 removed outlier: 4.445A pdb=" N ASN C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 300 Processing helix chain 'C' and resid 304 through 334 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 417 Processing helix chain 'C' and resid 419 through 437 Processing helix chain 'C' and resid 442 through 456 Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 473 through 488 removed outlier: 5.462A pdb=" N GLU C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 592 through 600 Processing helix chain 'C' and resid 603 through 618 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 120 through 144 Processing helix chain 'D' and resid 194 through 223 removed outlier: 6.596A pdb=" N HIS D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 246 Processing helix chain 'D' and resid 249 through 257 removed outlier: 4.104A pdb=" N LEU D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 262 Processing helix chain 'D' and resid 277 through 285 removed outlier: 4.446A pdb=" N ASN D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 300 Processing helix chain 'D' and resid 304 through 334 Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 386 through 417 Processing helix chain 'D' and resid 419 through 437 Processing helix chain 'D' and resid 442 through 456 Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 473 through 488 removed outlier: 5.463A pdb=" N GLU D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 592 through 600 Processing helix chain 'D' and resid 603 through 618 Processing sheet with id= A, first strand: chain 'A' and resid 185 through 188 Processing sheet with id= B, first strand: chain 'A' and resid 510 through 514 Processing sheet with id= C, first strand: chain 'A' and resid 538 through 540 Processing sheet with id= D, first strand: chain 'B' and resid 185 through 188 Processing sheet with id= E, first strand: chain 'B' and resid 510 through 514 Processing sheet with id= F, first strand: chain 'B' and resid 538 through 540 Processing sheet with id= G, first strand: chain 'C' and resid 185 through 188 Processing sheet with id= H, first strand: chain 'C' and resid 510 through 514 Processing sheet with id= I, first strand: chain 'C' and resid 538 through 540 Processing sheet with id= J, first strand: chain 'D' and resid 185 through 188 Processing sheet with id= K, first strand: chain 'D' and resid 510 through 514 Processing sheet with id= L, first strand: chain 'D' and resid 538 through 540 892 hydrogen bonds defined for protein. 2568 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: 5.12 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.19: 84 1.19 - 1.34: 5260 1.34 - 1.50: 5641 1.50 - 1.65: 6899 1.65 - 1.81: 156 Bond restraints: 18040 Sorted by residual: bond pdb=" C LEU A 394 " pdb=" O LEU A 394 " ideal model delta sigma weight residual 1.237 1.038 0.199 1.17e-02 7.31e+03 2.89e+02 bond pdb=" C LEU B 394 " pdb=" O LEU B 394 " ideal model delta sigma weight residual 1.237 1.038 0.199 1.17e-02 7.31e+03 2.88e+02 bond pdb=" C LEU D 394 " pdb=" O LEU D 394 " ideal model delta sigma weight residual 1.237 1.038 0.199 1.17e-02 7.31e+03 2.88e+02 bond pdb=" C LEU C 394 " pdb=" O LEU C 394 " ideal model delta sigma weight residual 1.237 1.038 0.199 1.17e-02 7.31e+03 2.88e+02 bond pdb=" C LEU D 396 " pdb=" O LEU D 396 " ideal model delta sigma weight residual 1.236 1.056 0.181 1.26e-02 6.30e+03 2.06e+02 ... (remaining 18035 not shown) Histogram of bond angle deviations from ideal: 92.22 - 100.88: 78 100.88 - 109.55: 1765 109.55 - 118.21: 11888 118.21 - 126.87: 10260 126.87 - 135.54: 309 Bond angle restraints: 24300 Sorted by residual: angle pdb=" C ASN B 292 " pdb=" CA ASN B 292 " pdb=" CB ASN B 292 " ideal model delta sigma weight residual 110.88 93.62 17.26 1.57e+00 4.06e-01 1.21e+02 angle pdb=" C ASN A 292 " pdb=" CA ASN A 292 " pdb=" CB ASN A 292 " ideal model delta sigma weight residual 110.88 93.65 17.23 1.57e+00 4.06e-01 1.20e+02 angle pdb=" C ASN D 292 " pdb=" CA ASN D 292 " pdb=" CB ASN D 292 " ideal model delta sigma weight residual 110.88 93.67 17.21 1.57e+00 4.06e-01 1.20e+02 angle pdb=" C ASN C 292 " pdb=" CA ASN C 292 " pdb=" CB ASN C 292 " ideal model delta sigma weight residual 110.88 93.67 17.21 1.57e+00 4.06e-01 1.20e+02 angle pdb=" N ASN C 571 " pdb=" CA ASN C 571 " pdb=" C ASN C 571 " ideal model delta sigma weight residual 107.28 124.59 -17.31 1.75e+00 3.27e-01 9.78e+01 ... (remaining 24295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.08: 10143 28.08 - 56.15: 553 56.15 - 84.23: 76 84.23 - 112.31: 12 112.31 - 140.38: 16 Dihedral angle restraints: 10800 sinusoidal: 4744 harmonic: 6056 Sorted by residual: dihedral pdb=" C ASN C 292 " pdb=" N ASN C 292 " pdb=" CA ASN C 292 " pdb=" CB ASN C 292 " ideal model delta harmonic sigma weight residual -122.60 -103.95 -18.65 0 2.50e+00 1.60e-01 5.56e+01 dihedral pdb=" C ASN A 292 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " pdb=" CB ASN A 292 " ideal model delta harmonic sigma weight residual -122.60 -103.96 -18.64 0 2.50e+00 1.60e-01 5.56e+01 dihedral pdb=" C ASN B 292 " pdb=" N ASN B 292 " pdb=" CA ASN B 292 " pdb=" CB ASN B 292 " ideal model delta harmonic sigma weight residual -122.60 -103.97 -18.63 0 2.50e+00 1.60e-01 5.56e+01 ... (remaining 10797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2397 0.082 - 0.164: 175 0.164 - 0.246: 34 0.246 - 0.328: 10 0.328 - 0.410: 8 Chirality restraints: 2624 Sorted by residual: chirality pdb=" CG LEU B 396 " pdb=" CB LEU B 396 " pdb=" CD1 LEU B 396 " pdb=" CD2 LEU B 396 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CG LEU C 396 " pdb=" CB LEU C 396 " pdb=" CD1 LEU C 396 " pdb=" CD2 LEU C 396 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CG LEU A 396 " pdb=" CB LEU A 396 " pdb=" CD1 LEU A 396 " pdb=" CD2 LEU A 396 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 2621 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 395 " 0.019 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ASP C 395 " -0.064 2.00e-02 2.50e+03 pdb=" O ASP C 395 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU C 396 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 395 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ASP B 395 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP B 395 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU B 396 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 395 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ASP D 395 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP D 395 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU D 396 " 0.021 2.00e-02 2.50e+03 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 413 2.66 - 3.22: 16120 3.22 - 3.78: 27094 3.78 - 4.34: 38775 4.34 - 4.90: 63582 Nonbonded interactions: 145984 Sorted by model distance: nonbonded pdb=" O ASN C 571 " pdb=" ND2 ASN C 571 " model vdw 2.097 2.520 nonbonded pdb=" O ASN D 571 " pdb=" ND2 ASN D 571 " model vdw 2.097 2.520 nonbonded pdb=" O ASN A 571 " pdb=" ND2 ASN A 571 " model vdw 2.097 2.520 nonbonded pdb=" O ASN B 571 " pdb=" ND2 ASN B 571 " model vdw 2.098 2.520 nonbonded pdb=" OD2 ASP C 212 " pdb=" OH TYR C 262 " model vdw 2.106 2.440 ... (remaining 145979 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' and (resid 104 through 619 or resid 801 through 808)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.690 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 47.410 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.110 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.015 0.229 18040 Z= 0.958 Angle : 1.488 21.660 24300 Z= 0.723 Chirality : 0.057 0.410 2624 Planarity : 0.006 0.040 2952 Dihedral : 17.567 140.382 6900 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.80 % Allowed : 7.31 % Favored : 89.89 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.16), residues: 2036 helix: -0.74 (0.13), residues: 1180 sheet: -0.65 (0.45), residues: 124 loop : -2.37 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 596 HIS 0.003 0.002 HIS D 321 PHE 0.017 0.002 PHE C 138 TYR 0.017 0.002 TYR B 363 ARG 0.003 0.001 ARG D 580 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 283 time to evaluate : 2.191 Fit side-chains revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7821 (mtm-85) REVERT: A 180 MET cc_start: 0.8949 (mtm) cc_final: 0.8625 (mtp) REVERT: A 202 MET cc_start: 0.7296 (ttp) cc_final: 0.6895 (mmt) REVERT: A 224 ARG cc_start: 0.8086 (mmt90) cc_final: 0.7833 (mmt90) REVERT: A 291 ARG cc_start: 0.7050 (mmm160) cc_final: 0.6805 (mmm160) REVERT: A 303 MET cc_start: 0.7328 (mtm) cc_final: 0.6173 (mmm) REVERT: A 395 ASP cc_start: 0.9477 (OUTLIER) cc_final: 0.9267 (t0) REVERT: A 433 GLN cc_start: 0.7456 (tt0) cc_final: 0.7170 (tt0) REVERT: A 443 GLN cc_start: 0.6525 (tm-30) cc_final: 0.6301 (tp40) REVERT: A 452 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: A 529 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: A 535 ARG cc_start: 0.6592 (mtt180) cc_final: 0.6019 (mmm160) REVERT: A 607 LYS cc_start: 0.8703 (mttp) cc_final: 0.8259 (mptt) REVERT: A 609 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5265 (mp) REVERT: B 158 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7874 (mtp180) REVERT: B 202 MET cc_start: 0.7127 (ttp) cc_final: 0.6676 (mmt) REVERT: B 303 MET cc_start: 0.7479 (mtm) cc_final: 0.6321 (mmm) REVERT: B 433 GLN cc_start: 0.7626 (tt0) cc_final: 0.7376 (tt0) REVERT: B 442 LYS cc_start: 0.7639 (mmmt) cc_final: 0.6871 (ttpp) REVERT: B 443 GLN cc_start: 0.6885 (tm-30) cc_final: 0.6650 (tm-30) REVERT: B 530 MET cc_start: 0.8350 (ttp) cc_final: 0.8095 (ttm) REVERT: C 158 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7862 (mtp180) REVERT: C 180 MET cc_start: 0.8934 (mtm) cc_final: 0.8626 (mtp) REVERT: C 202 MET cc_start: 0.7205 (ttp) cc_final: 0.6834 (mmt) REVERT: C 291 ARG cc_start: 0.7053 (mmm160) cc_final: 0.6811 (mmm160) REVERT: C 303 MET cc_start: 0.7289 (mtm) cc_final: 0.6150 (mmm) REVERT: C 433 GLN cc_start: 0.7416 (tt0) cc_final: 0.7113 (tt0) REVERT: C 452 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: C 529 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: C 530 MET cc_start: 0.8385 (ttp) cc_final: 0.8104 (ttm) REVERT: C 606 ARG cc_start: 0.7276 (ttp-110) cc_final: 0.7060 (ttm110) REVERT: C 609 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5405 (mp) REVERT: D 158 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7838 (mtp180) REVERT: D 202 MET cc_start: 0.7016 (ttp) cc_final: 0.6663 (mmt) REVERT: D 251 ARG cc_start: 0.7076 (mtt90) cc_final: 0.6784 (mtm-85) REVERT: D 291 ARG cc_start: 0.7013 (mmm160) cc_final: 0.6802 (mmm160) REVERT: D 303 MET cc_start: 0.7435 (mtm) cc_final: 0.6285 (mmm) REVERT: D 433 GLN cc_start: 0.7299 (tt0) cc_final: 0.6990 (tt0) REVERT: D 442 LYS cc_start: 0.7344 (mmmt) cc_final: 0.6954 (tttm) REVERT: D 452 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: D 525 ASP cc_start: 0.7351 (t70) cc_final: 0.6773 (t0) REVERT: D 529 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7247 (mm-30) REVERT: D 530 MET cc_start: 0.8361 (ttp) cc_final: 0.8129 (ttm) REVERT: D 606 ARG cc_start: 0.7265 (ttp-110) cc_final: 0.7039 (ttm110) REVERT: D 607 LYS cc_start: 0.8943 (mttp) cc_final: 0.8667 (mptt) outliers start: 52 outliers final: 5 residues processed: 321 average time/residue: 1.4073 time to fit residues: 498.9768 Evaluate side-chains 250 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 529 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS A 386 ASN A 416 ASN A 425 GLN A 482 GLN A 512 GLN A 539 GLN A 578 ASN B 114 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS B 386 ASN B 416 ASN B 425 GLN B 426 ASN B 482 GLN B 512 GLN B 539 GLN B 578 ASN C 114 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS C 386 ASN C 416 ASN C 425 GLN C 482 GLN C 512 GLN C 539 GLN C 578 ASN D 114 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 HIS D 386 ASN D 416 ASN D 425 GLN D 482 GLN D 512 GLN D 539 GLN D 578 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18040 Z= 0.182 Angle : 0.563 15.238 24300 Z= 0.290 Chirality : 0.040 0.216 2624 Planarity : 0.004 0.045 2952 Dihedral : 16.816 124.634 2847 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.96 % Allowed : 11.08 % Favored : 85.97 % 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: -0.41 (0.18), residues: 2036 helix: 0.59 (0.14), residues: 1200 sheet: -0.09 (0.53), residues: 104 loop : -1.72 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 596 HIS 0.003 0.001 HIS D 321 PHE 0.018 0.001 PHE A 138 TYR 0.018 0.001 TYR A 434 ARG 0.005 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 274 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7943 (mtp180) REVERT: A 202 MET cc_start: 0.7228 (ttp) cc_final: 0.6868 (mmt) REVERT: A 239 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7760 (mtmt) REVERT: A 291 ARG cc_start: 0.7018 (mmm160) cc_final: 0.6482 (mtm110) REVERT: A 303 MET cc_start: 0.7230 (mtm) cc_final: 0.6070 (mmm) REVERT: A 433 GLN cc_start: 0.7383 (tt0) cc_final: 0.7081 (tt0) REVERT: A 443 GLN cc_start: 0.6614 (tm-30) cc_final: 0.6315 (tp40) REVERT: A 452 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: A 482 GLN cc_start: 0.7801 (tt0) cc_final: 0.7369 (tt0) REVERT: A 489 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7795 (tpt170) REVERT: A 512 GLN cc_start: 0.7347 (mt0) cc_final: 0.7074 (mt0) REVERT: A 529 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6721 (mm-30) REVERT: B 158 ARG cc_start: 0.8129 (mtt90) cc_final: 0.7800 (mtm-85) REVERT: B 202 MET cc_start: 0.7054 (ttp) cc_final: 0.6656 (mmt) REVERT: B 224 ARG cc_start: 0.7938 (mmt90) cc_final: 0.7619 (mmt90) REVERT: B 274 ARG cc_start: 0.7542 (ptp-110) cc_final: 0.7126 (pmt170) REVERT: B 303 MET cc_start: 0.7381 (mtm) cc_final: 0.6274 (mmm) REVERT: B 423 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: B 433 GLN cc_start: 0.7526 (tt0) cc_final: 0.7202 (tt0) REVERT: B 442 LYS cc_start: 0.7544 (mmmt) cc_final: 0.6932 (tttm) REVERT: B 443 GLN cc_start: 0.6714 (tm-30) cc_final: 0.6477 (tm-30) REVERT: B 482 GLN cc_start: 0.7743 (tt0) cc_final: 0.7281 (tt0) REVERT: B 489 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7804 (tpt170) REVERT: B 507 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6947 (mm) REVERT: C 158 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7872 (mtp180) REVERT: C 202 MET cc_start: 0.7243 (ttp) cc_final: 0.6893 (mmt) REVERT: C 291 ARG cc_start: 0.7140 (mmm160) cc_final: 0.6600 (mtm110) REVERT: C 303 MET cc_start: 0.7230 (mtm) cc_final: 0.6107 (mmm) REVERT: C 433 GLN cc_start: 0.7384 (tt0) cc_final: 0.7060 (tt0) REVERT: C 452 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: C 489 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7816 (tpt170) REVERT: C 512 GLN cc_start: 0.7322 (mt0) cc_final: 0.7032 (mt0) REVERT: C 523 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7859 (mtmm) REVERT: C 606 ARG cc_start: 0.7120 (ttp-110) cc_final: 0.6898 (ttm110) REVERT: D 158 ARG cc_start: 0.8110 (mtt90) cc_final: 0.7868 (mtp180) REVERT: D 202 MET cc_start: 0.6932 (ttp) cc_final: 0.6635 (mmt) REVERT: D 211 MET cc_start: 0.8166 (mmt) cc_final: 0.7943 (mmm) REVERT: D 224 ARG cc_start: 0.7865 (mmt90) cc_final: 0.7510 (mmt90) REVERT: D 251 ARG cc_start: 0.6997 (mtt90) cc_final: 0.6693 (mtm-85) REVERT: D 274 ARG cc_start: 0.7433 (ptp-110) cc_final: 0.6975 (pmt170) REVERT: D 291 ARG cc_start: 0.7090 (mmm160) cc_final: 0.6601 (mtm110) REVERT: D 303 MET cc_start: 0.7214 (mtm) cc_final: 0.6084 (mmm) REVERT: D 433 GLN cc_start: 0.7352 (tt0) cc_final: 0.6951 (tt0) REVERT: D 442 LYS cc_start: 0.7272 (mmmt) cc_final: 0.6888 (tttm) REVERT: D 452 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: D 482 GLN cc_start: 0.7740 (tt0) cc_final: 0.7364 (tt0) REVERT: D 512 GLN cc_start: 0.7359 (mt0) cc_final: 0.7077 (mt0) REVERT: D 525 ASP cc_start: 0.7319 (t70) cc_final: 0.6739 (t0) REVERT: D 529 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6864 (mm-30) outliers start: 55 outliers final: 9 residues processed: 304 average time/residue: 1.3967 time to fit residues: 470.5900 Evaluate side-chains 268 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 247 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 489 ARG Chi-restraints excluded: chain C residue 523 LYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 529 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 8.9990 chunk 57 optimal weight: 0.0970 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 0.4980 chunk 51 optimal weight: 8.9990 chunk 185 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18040 Z= 0.214 Angle : 0.550 15.085 24300 Z= 0.283 Chirality : 0.041 0.212 2624 Planarity : 0.004 0.046 2952 Dihedral : 15.544 124.204 2838 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.33 % Allowed : 13.12 % Favored : 83.55 % 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: 0.22 (0.18), residues: 2036 helix: 1.09 (0.15), residues: 1196 sheet: 1.09 (0.52), residues: 96 loop : -1.57 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 596 HIS 0.003 0.001 HIS B 321 PHE 0.018 0.002 PHE A 138 TYR 0.020 0.002 TYR B 434 ARG 0.007 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 254 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7946 (mtp180) REVERT: A 202 MET cc_start: 0.7224 (ttp) cc_final: 0.6873 (mmt) REVERT: A 274 ARG cc_start: 0.7538 (ptp-110) cc_final: 0.7034 (pmt170) REVERT: A 291 ARG cc_start: 0.7066 (mmm160) cc_final: 0.6842 (mmm160) REVERT: A 303 MET cc_start: 0.7159 (mtm) cc_final: 0.6030 (mmm) REVERT: A 423 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: A 433 GLN cc_start: 0.7468 (tt0) cc_final: 0.7087 (tt0) REVERT: A 442 LYS cc_start: 0.7302 (mmmt) cc_final: 0.6922 (tttm) REVERT: A 452 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: A 482 GLN cc_start: 0.7794 (tt0) cc_final: 0.7292 (tt0) REVERT: A 489 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7725 (tpt170) REVERT: A 512 GLN cc_start: 0.7311 (mt0) cc_final: 0.7030 (mt0) REVERT: B 202 MET cc_start: 0.7186 (ttp) cc_final: 0.6847 (mmt) REVERT: B 228 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8118 (tpp) REVERT: B 251 ARG cc_start: 0.7104 (mtt90) cc_final: 0.6758 (mtm-85) REVERT: B 274 ARG cc_start: 0.7512 (ptp-110) cc_final: 0.7118 (pmt170) REVERT: B 303 MET cc_start: 0.7276 (mtm) cc_final: 0.6205 (mmm) REVERT: B 433 GLN cc_start: 0.7526 (tt0) cc_final: 0.7220 (tt0) REVERT: B 442 LYS cc_start: 0.7519 (mmmt) cc_final: 0.6978 (tttm) REVERT: B 443 GLN cc_start: 0.6640 (tm-30) cc_final: 0.6301 (tp-100) REVERT: B 489 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7605 (tpm170) REVERT: C 158 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7880 (mtp180) REVERT: C 202 MET cc_start: 0.7225 (ttp) cc_final: 0.6874 (mmt) REVERT: C 274 ARG cc_start: 0.7530 (ptp-110) cc_final: 0.7035 (pmt170) REVERT: C 291 ARG cc_start: 0.7036 (mmm160) cc_final: 0.6556 (mtm-85) REVERT: C 303 MET cc_start: 0.7126 (mtm) cc_final: 0.6001 (mmm) REVERT: C 423 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: C 433 GLN cc_start: 0.7436 (tt0) cc_final: 0.7069 (tt0) REVERT: C 442 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6841 (tttm) REVERT: C 452 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: C 482 GLN cc_start: 0.7808 (tt0) cc_final: 0.7338 (tt0) REVERT: C 489 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7753 (tpt170) REVERT: C 512 GLN cc_start: 0.7261 (mt0) cc_final: 0.6955 (mt0) REVERT: C 530 MET cc_start: 0.7815 (ttp) cc_final: 0.7572 (ttt) REVERT: D 158 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7875 (mtp180) REVERT: D 202 MET cc_start: 0.7016 (ttp) cc_final: 0.6720 (mmt) REVERT: D 211 MET cc_start: 0.8136 (mmt) cc_final: 0.7865 (mmm) REVERT: D 224 ARG cc_start: 0.7895 (mmt90) cc_final: 0.7567 (mmt90) REVERT: D 251 ARG cc_start: 0.7031 (mtt90) cc_final: 0.6603 (mtm-85) REVERT: D 274 ARG cc_start: 0.7495 (ptp-110) cc_final: 0.7017 (pmt170) REVERT: D 291 ARG cc_start: 0.7077 (mmm160) cc_final: 0.6861 (mmm160) REVERT: D 303 MET cc_start: 0.7129 (mtm) cc_final: 0.6009 (mmm) REVERT: D 433 GLN cc_start: 0.7393 (tt0) cc_final: 0.7085 (tt0) REVERT: D 442 LYS cc_start: 0.7339 (mmmt) cc_final: 0.6951 (tttm) REVERT: D 452 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: D 489 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7577 (tpm170) REVERT: D 512 GLN cc_start: 0.7309 (mt0) cc_final: 0.7038 (mt0) outliers start: 62 outliers final: 16 residues processed: 283 average time/residue: 1.3558 time to fit residues: 426.4549 Evaluate side-chains 261 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 235 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 ARG Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 489 ARG Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 489 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 97 optimal weight: 0.0970 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 169 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18040 Z= 0.195 Angle : 0.519 13.055 24300 Z= 0.270 Chirality : 0.040 0.209 2624 Planarity : 0.004 0.045 2952 Dihedral : 14.461 123.974 2832 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.39 % Allowed : 14.73 % Favored : 81.88 % 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: 0.53 (0.18), residues: 2036 helix: 1.33 (0.15), residues: 1196 sheet: 1.35 (0.51), residues: 96 loop : -1.44 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 451 HIS 0.002 0.001 HIS A 321 PHE 0.017 0.001 PHE A 138 TYR 0.021 0.001 TYR B 434 ARG 0.005 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 249 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7949 (mtp180) REVERT: A 202 MET cc_start: 0.7213 (ttp) cc_final: 0.6878 (mmt) REVERT: A 251 ARG cc_start: 0.7082 (mtt90) cc_final: 0.6672 (mtm-85) REVERT: A 274 ARG cc_start: 0.7525 (ptp-110) cc_final: 0.7029 (pmt170) REVERT: A 303 MET cc_start: 0.7114 (mtm) cc_final: 0.5995 (mmm) REVERT: A 423 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: A 433 GLN cc_start: 0.7447 (tt0) cc_final: 0.7095 (tt0) REVERT: A 442 LYS cc_start: 0.7338 (mmmt) cc_final: 0.6897 (tttm) REVERT: A 452 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: A 482 GLN cc_start: 0.7785 (tt0) cc_final: 0.7287 (tt0) REVERT: A 489 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7752 (tpt170) REVERT: A 512 GLN cc_start: 0.7224 (mt0) cc_final: 0.6919 (mt0) REVERT: B 202 MET cc_start: 0.7177 (ttp) cc_final: 0.6848 (mmt) REVERT: B 224 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7454 (mmt90) REVERT: B 228 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8115 (tpp) REVERT: B 251 ARG cc_start: 0.7093 (mtt90) cc_final: 0.6789 (mtm-85) REVERT: B 274 ARG cc_start: 0.7450 (ptp-110) cc_final: 0.7060 (pmt170) REVERT: B 303 MET cc_start: 0.7128 (mtm) cc_final: 0.6010 (mmm) REVERT: B 423 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: B 433 GLN cc_start: 0.7521 (tt0) cc_final: 0.7240 (tt0) REVERT: B 442 LYS cc_start: 0.7476 (mmmt) cc_final: 0.6915 (tttm) REVERT: B 443 GLN cc_start: 0.6627 (tm-30) cc_final: 0.6300 (tp-100) REVERT: B 482 GLN cc_start: 0.7789 (tt0) cc_final: 0.7268 (tt0) REVERT: C 158 ARG cc_start: 0.8133 (mtt90) cc_final: 0.7889 (mtp180) REVERT: C 202 MET cc_start: 0.7213 (ttp) cc_final: 0.6877 (mmt) REVERT: C 251 ARG cc_start: 0.7074 (mtt90) cc_final: 0.6664 (mtm-85) REVERT: C 274 ARG cc_start: 0.7522 (ptp-110) cc_final: 0.7030 (pmt170) REVERT: C 303 MET cc_start: 0.7133 (mtm) cc_final: 0.6078 (mmm) REVERT: C 433 GLN cc_start: 0.7441 (tt0) cc_final: 0.7095 (tt0) REVERT: C 442 LYS cc_start: 0.7322 (mmmt) cc_final: 0.6875 (tttm) REVERT: C 452 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: C 489 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7716 (tpt170) REVERT: C 530 MET cc_start: 0.7772 (ttp) cc_final: 0.7507 (ttt) REVERT: C 609 LEU cc_start: 0.5546 (OUTLIER) cc_final: 0.5286 (mp) REVERT: D 158 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7913 (mtp180) REVERT: D 202 MET cc_start: 0.6988 (ttp) cc_final: 0.6696 (mmt) REVERT: D 211 MET cc_start: 0.8126 (mmt) cc_final: 0.7888 (mmm) REVERT: D 224 ARG cc_start: 0.7880 (mmt90) cc_final: 0.7560 (mmt90) REVERT: D 251 ARG cc_start: 0.7107 (mtt90) cc_final: 0.6695 (mtm-85) REVERT: D 274 ARG cc_start: 0.7443 (ptp-110) cc_final: 0.6997 (pmt170) REVERT: D 291 ARG cc_start: 0.7047 (mmm160) cc_final: 0.6821 (mmm160) REVERT: D 303 MET cc_start: 0.7053 (mtm) cc_final: 0.5978 (mmm) REVERT: D 433 GLN cc_start: 0.7428 (tt0) cc_final: 0.7122 (tt0) REVERT: D 442 LYS cc_start: 0.7370 (mmmt) cc_final: 0.6959 (tttm) REVERT: D 452 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: D 489 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7461 (tpm170) REVERT: D 512 GLN cc_start: 0.7266 (mt0) cc_final: 0.7011 (mt0) outliers start: 63 outliers final: 22 residues processed: 278 average time/residue: 1.3741 time to fit residues: 423.7606 Evaluate side-chains 280 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 248 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 489 ARG Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 489 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 18040 Z= 0.391 Angle : 0.623 13.227 24300 Z= 0.322 Chirality : 0.045 0.215 2624 Planarity : 0.004 0.043 2952 Dihedral : 14.782 125.978 2832 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.66 % Allowed : 15.38 % Favored : 80.97 % 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: 0.47 (0.18), residues: 2036 helix: 1.22 (0.15), residues: 1176 sheet: 1.31 (0.51), residues: 96 loop : -1.25 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 596 HIS 0.004 0.002 HIS D 199 PHE 0.020 0.002 PHE A 138 TYR 0.022 0.002 TYR B 434 ARG 0.005 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 241 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8206 (mtt90) cc_final: 0.8003 (mtp180) REVERT: A 202 MET cc_start: 0.7053 (ttp) cc_final: 0.6765 (mmt) REVERT: A 251 ARG cc_start: 0.7115 (mtt90) cc_final: 0.6732 (mtm-85) REVERT: A 291 ARG cc_start: 0.7004 (mmm160) cc_final: 0.6493 (mtm110) REVERT: A 303 MET cc_start: 0.7188 (mtm) cc_final: 0.6050 (mmm) REVERT: A 423 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: A 433 GLN cc_start: 0.7469 (tt0) cc_final: 0.7085 (tt0) REVERT: A 442 LYS cc_start: 0.7423 (mmmt) cc_final: 0.6943 (tttm) REVERT: A 452 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: A 489 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7823 (tpt170) REVERT: A 599 LEU cc_start: 0.7240 (mp) cc_final: 0.6993 (mp) REVERT: A 606 ARG cc_start: 0.7004 (ttm110) cc_final: 0.6770 (ttm110) REVERT: B 202 MET cc_start: 0.7052 (ttp) cc_final: 0.6766 (mmt) REVERT: B 224 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7667 (mmt90) REVERT: B 251 ARG cc_start: 0.7105 (mtt90) cc_final: 0.6765 (mtm-85) REVERT: B 303 MET cc_start: 0.7167 (mtm) cc_final: 0.6001 (mmm) REVERT: B 423 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: B 433 GLN cc_start: 0.7546 (tt0) cc_final: 0.7198 (tt0) REVERT: B 442 LYS cc_start: 0.7617 (mmmt) cc_final: 0.7126 (tttm) REVERT: B 443 GLN cc_start: 0.6816 (tm-30) cc_final: 0.6522 (tp-100) REVERT: B 489 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7624 (tpm170) REVERT: C 158 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7979 (mtp180) REVERT: C 202 MET cc_start: 0.7052 (ttp) cc_final: 0.6765 (mmt) REVERT: C 251 ARG cc_start: 0.7140 (mtt90) cc_final: 0.6744 (mtm-85) REVERT: C 291 ARG cc_start: 0.7024 (mmm160) cc_final: 0.6479 (mtm110) REVERT: C 303 MET cc_start: 0.7190 (mtm) cc_final: 0.6055 (mmm) REVERT: C 433 GLN cc_start: 0.7478 (tt0) cc_final: 0.7083 (tt0) REVERT: C 442 LYS cc_start: 0.7486 (mmmt) cc_final: 0.7026 (tttm) REVERT: C 452 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: C 489 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7772 (tpt170) REVERT: C 609 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5267 (mp) REVERT: D 158 ARG cc_start: 0.8162 (mtt90) cc_final: 0.7960 (mtp180) REVERT: D 202 MET cc_start: 0.6975 (ttp) cc_final: 0.6658 (mmt) REVERT: D 224 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7734 (mmt90) REVERT: D 251 ARG cc_start: 0.7139 (mtt90) cc_final: 0.6726 (mtm-85) REVERT: D 303 MET cc_start: 0.7181 (mtm) cc_final: 0.6058 (mmm) REVERT: D 433 GLN cc_start: 0.7454 (tt0) cc_final: 0.7109 (tt0) REVERT: D 442 LYS cc_start: 0.7388 (mmmt) cc_final: 0.6921 (tttm) REVERT: D 452 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: D 489 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7776 (tpt170) outliers start: 68 outliers final: 28 residues processed: 275 average time/residue: 1.4100 time to fit residues: 430.6852 Evaluate side-chains 278 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 240 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 489 ARG Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 489 ARG Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 489 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 91 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18040 Z= 0.204 Angle : 0.530 12.641 24300 Z= 0.277 Chirality : 0.041 0.200 2624 Planarity : 0.004 0.046 2952 Dihedral : 13.816 124.171 2832 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.17 % Allowed : 16.45 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2036 helix: 1.37 (0.14), residues: 1192 sheet: 1.45 (0.49), residues: 96 loop : -1.30 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 451 HIS 0.003 0.001 HIS B 321 PHE 0.017 0.001 PHE B 138 TYR 0.024 0.001 TYR B 434 ARG 0.004 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 247 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7139 (ttp) cc_final: 0.6794 (mmt) REVERT: A 228 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8336 (tpt) REVERT: A 251 ARG cc_start: 0.7119 (mtt90) cc_final: 0.6719 (mtm-85) REVERT: A 274 ARG cc_start: 0.7530 (ptp-110) cc_final: 0.7031 (pmt170) REVERT: A 291 ARG cc_start: 0.7007 (mmm160) cc_final: 0.6525 (mtm110) REVERT: A 303 MET cc_start: 0.7107 (mtm) cc_final: 0.6007 (mmm) REVERT: A 433 GLN cc_start: 0.7418 (tt0) cc_final: 0.7103 (tt0) REVERT: A 442 LYS cc_start: 0.7400 (mmmt) cc_final: 0.6861 (tttm) REVERT: A 489 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7653 (tpt170) REVERT: A 539 GLN cc_start: 0.8004 (pt0) cc_final: 0.7794 (pt0) REVERT: B 202 MET cc_start: 0.7137 (ttp) cc_final: 0.6795 (mmt) REVERT: B 251 ARG cc_start: 0.7050 (mtt90) cc_final: 0.6744 (mtm-85) REVERT: B 274 ARG cc_start: 0.7480 (ptp-110) cc_final: 0.7090 (pmt170) REVERT: B 303 MET cc_start: 0.7100 (mtm) cc_final: 0.6003 (mmm) REVERT: B 423 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6921 (tt0) REVERT: B 433 GLN cc_start: 0.7384 (tt0) cc_final: 0.7065 (tt0) REVERT: B 442 LYS cc_start: 0.7406 (mmmt) cc_final: 0.6904 (tttm) REVERT: B 443 GLN cc_start: 0.6701 (tm-30) cc_final: 0.6423 (tp-100) REVERT: B 489 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7534 (tpm170) REVERT: B 539 GLN cc_start: 0.7942 (pt0) cc_final: 0.7704 (pt0) REVERT: C 202 MET cc_start: 0.7136 (ttp) cc_final: 0.6793 (mmt) REVERT: C 251 ARG cc_start: 0.7134 (mtt90) cc_final: 0.6714 (mtm-85) REVERT: C 274 ARG cc_start: 0.7528 (ptp-110) cc_final: 0.7034 (pmt170) REVERT: C 291 ARG cc_start: 0.7005 (mmm160) cc_final: 0.6524 (mtm110) REVERT: C 303 MET cc_start: 0.7104 (mtm) cc_final: 0.6008 (mmm) REVERT: C 433 GLN cc_start: 0.7402 (tt0) cc_final: 0.7040 (tt0) REVERT: C 442 LYS cc_start: 0.7389 (mmmt) cc_final: 0.6839 (tttm) REVERT: C 452 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: C 489 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7569 (tpm170) REVERT: C 606 ARG cc_start: 0.7482 (ttp-110) cc_final: 0.7219 (ttm110) REVERT: C 609 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5375 (mp) REVERT: D 202 MET cc_start: 0.7086 (ttp) cc_final: 0.6754 (mmt) REVERT: D 251 ARG cc_start: 0.7088 (mtt90) cc_final: 0.6705 (mtm-85) REVERT: D 274 ARG cc_start: 0.7522 (ptp-110) cc_final: 0.7043 (pmt170) REVERT: D 291 ARG cc_start: 0.6994 (mmm160) cc_final: 0.6476 (mtm110) REVERT: D 303 MET cc_start: 0.7062 (mtm) cc_final: 0.5955 (mmm) REVERT: D 433 GLN cc_start: 0.7367 (tt0) cc_final: 0.7023 (tt0) REVERT: D 442 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6850 (tttm) REVERT: D 452 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: D 489 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7481 (tpm170) REVERT: D 492 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7889 (ttp-110) REVERT: D 539 GLN cc_start: 0.7940 (pt0) cc_final: 0.7690 (pt0) outliers start: 59 outliers final: 28 residues processed: 280 average time/residue: 1.3783 time to fit residues: 427.7871 Evaluate side-chains 277 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 240 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 489 ARG Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 489 ARG Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 489 ARG Chi-restraints excluded: chain D residue 515 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 196 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 119 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 HIS ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18040 Z= 0.181 Angle : 0.516 12.153 24300 Z= 0.271 Chirality : 0.040 0.183 2624 Planarity : 0.004 0.048 2952 Dihedral : 13.192 123.016 2826 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.17 % Allowed : 17.37 % Favored : 79.46 % 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: 0.82 (0.18), residues: 2036 helix: 1.53 (0.14), residues: 1188 sheet: 1.83 (0.48), residues: 96 loop : -1.27 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 451 HIS 0.003 0.001 HIS B 321 PHE 0.018 0.001 PHE A 138 TYR 0.024 0.001 TYR B 434 ARG 0.010 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 245 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7182 (ttp) cc_final: 0.6854 (mmt) REVERT: A 228 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8376 (tpt) REVERT: A 251 ARG cc_start: 0.7097 (mtt90) cc_final: 0.6727 (mtm-85) REVERT: A 274 ARG cc_start: 0.7471 (ptp-110) cc_final: 0.6975 (pmt170) REVERT: A 291 ARG cc_start: 0.7008 (mmm160) cc_final: 0.6526 (mtm110) REVERT: A 303 MET cc_start: 0.7016 (mtm) cc_final: 0.5931 (mmm) REVERT: A 423 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6827 (tt0) REVERT: A 433 GLN cc_start: 0.7381 (tt0) cc_final: 0.7060 (tt0) REVERT: A 442 LYS cc_start: 0.7386 (mmmt) cc_final: 0.6845 (tttm) REVERT: A 489 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7598 (tpt170) REVERT: A 539 GLN cc_start: 0.7956 (pt0) cc_final: 0.7736 (pt0) REVERT: B 202 MET cc_start: 0.7154 (ttp) cc_final: 0.6773 (mmt) REVERT: B 251 ARG cc_start: 0.7005 (mtt90) cc_final: 0.6711 (mtm-85) REVERT: B 274 ARG cc_start: 0.7470 (ptp-110) cc_final: 0.7097 (pmt170) REVERT: B 303 MET cc_start: 0.7051 (mtm) cc_final: 0.5983 (mmm) REVERT: B 423 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: B 433 GLN cc_start: 0.7382 (tt0) cc_final: 0.7053 (tt0) REVERT: B 442 LYS cc_start: 0.7294 (mmmt) cc_final: 0.6782 (tttm) REVERT: B 443 GLN cc_start: 0.6669 (tm-30) cc_final: 0.6394 (tp40) REVERT: B 539 GLN cc_start: 0.7938 (pt0) cc_final: 0.7695 (pt0) REVERT: C 202 MET cc_start: 0.7120 (ttp) cc_final: 0.6754 (mmt) REVERT: C 251 ARG cc_start: 0.7149 (mtt90) cc_final: 0.6751 (mtm-85) REVERT: C 274 ARG cc_start: 0.7469 (ptp-110) cc_final: 0.6984 (pmt170) REVERT: C 291 ARG cc_start: 0.7004 (mmm160) cc_final: 0.6524 (mtm110) REVERT: C 303 MET cc_start: 0.7010 (mtm) cc_final: 0.5931 (mmm) REVERT: C 433 GLN cc_start: 0.7391 (tt0) cc_final: 0.7055 (tt0) REVERT: C 442 LYS cc_start: 0.7395 (mmmt) cc_final: 0.6844 (tttm) REVERT: C 452 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7419 (m-80) REVERT: C 489 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7588 (tpt170) REVERT: C 539 GLN cc_start: 0.8042 (pt0) cc_final: 0.7836 (pt0) REVERT: C 606 ARG cc_start: 0.7422 (ttp-110) cc_final: 0.7170 (ttm110) REVERT: D 202 MET cc_start: 0.7072 (ttp) cc_final: 0.6721 (mmt) REVERT: D 251 ARG cc_start: 0.7176 (mtt90) cc_final: 0.6759 (mtm-85) REVERT: D 274 ARG cc_start: 0.7437 (ptp-110) cc_final: 0.6973 (pmt170) REVERT: D 291 ARG cc_start: 0.7004 (mmm160) cc_final: 0.6525 (mtm110) REVERT: D 303 MET cc_start: 0.7012 (mtm) cc_final: 0.5962 (mmm) REVERT: D 433 GLN cc_start: 0.7387 (tt0) cc_final: 0.6974 (tt0) REVERT: D 442 LYS cc_start: 0.7407 (mmmt) cc_final: 0.6835 (tttm) REVERT: D 452 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: D 489 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7467 (tpm170) REVERT: D 492 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7823 (ttp-110) REVERT: D 539 GLN cc_start: 0.7890 (pt0) cc_final: 0.7649 (pt0) outliers start: 59 outliers final: 28 residues processed: 275 average time/residue: 1.3511 time to fit residues: 412.4198 Evaluate side-chains 281 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 245 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 489 ARG Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 489 ARG Chi-restraints excluded: chain D residue 515 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 0.0470 chunk 178 optimal weight: 0.6980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN A 484 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN C 484 HIS ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 484 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 18040 Z= 0.137 Angle : 0.493 15.060 24300 Z= 0.260 Chirality : 0.039 0.166 2624 Planarity : 0.004 0.045 2952 Dihedral : 12.407 120.937 2822 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.31 % Allowed : 18.71 % Favored : 78.98 % 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: 1.00 (0.18), residues: 2036 helix: 1.63 (0.15), residues: 1192 sheet: 2.09 (0.47), residues: 96 loop : -1.15 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 451 HIS 0.002 0.001 HIS B 321 PHE 0.017 0.001 PHE A 138 TYR 0.024 0.001 TYR C 434 ARG 0.011 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 252 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7137 (ttp) cc_final: 0.6803 (mmt) REVERT: A 251 ARG cc_start: 0.7107 (mtt90) cc_final: 0.6728 (mtm-85) REVERT: A 274 ARG cc_start: 0.7336 (ptp-110) cc_final: 0.6967 (pmt170) REVERT: A 291 ARG cc_start: 0.7006 (mmm160) cc_final: 0.6525 (mtm110) REVERT: A 303 MET cc_start: 0.6992 (mtm) cc_final: 0.5941 (mmm) REVERT: A 433 GLN cc_start: 0.7386 (tt0) cc_final: 0.7033 (tt0) REVERT: A 442 LYS cc_start: 0.7294 (mmmt) cc_final: 0.6730 (tttm) REVERT: A 452 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: A 548 VAL cc_start: 0.5278 (OUTLIER) cc_final: 0.4829 (m) REVERT: B 202 MET cc_start: 0.7135 (ttp) cc_final: 0.6803 (mmt) REVERT: B 251 ARG cc_start: 0.7037 (mtt90) cc_final: 0.6720 (mtm-85) REVERT: B 274 ARG cc_start: 0.7358 (ptp-110) cc_final: 0.7029 (pmt170) REVERT: B 291 ARG cc_start: 0.6967 (mmm160) cc_final: 0.6552 (mtm110) REVERT: B 303 MET cc_start: 0.7015 (mtm) cc_final: 0.5956 (mmm) REVERT: B 423 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6827 (tt0) REVERT: B 433 GLN cc_start: 0.7371 (tt0) cc_final: 0.7015 (tt0) REVERT: B 442 LYS cc_start: 0.7303 (mmmt) cc_final: 0.6768 (tttm) REVERT: B 443 GLN cc_start: 0.6601 (tm-30) cc_final: 0.6325 (tp40) REVERT: C 202 MET cc_start: 0.7133 (ttp) cc_final: 0.6802 (mmt) REVERT: C 211 MET cc_start: 0.8117 (mmt) cc_final: 0.7837 (mmm) REVERT: C 251 ARG cc_start: 0.7172 (mtt90) cc_final: 0.6755 (mtm-85) REVERT: C 274 ARG cc_start: 0.7338 (ptp-110) cc_final: 0.6969 (pmt170) REVERT: C 291 ARG cc_start: 0.7003 (mmm160) cc_final: 0.6523 (mtm110) REVERT: C 303 MET cc_start: 0.6984 (mtm) cc_final: 0.5885 (mmm) REVERT: C 433 GLN cc_start: 0.7272 (tt0) cc_final: 0.6947 (tt0) REVERT: C 442 LYS cc_start: 0.7417 (mmmt) cc_final: 0.6869 (tttm) REVERT: C 539 GLN cc_start: 0.7951 (pt0) cc_final: 0.7742 (pt0) REVERT: C 606 ARG cc_start: 0.7353 (ttp-110) cc_final: 0.7112 (ttm110) REVERT: D 202 MET cc_start: 0.7097 (ttp) cc_final: 0.6733 (mmt) REVERT: D 251 ARG cc_start: 0.7164 (mtt90) cc_final: 0.6735 (mtm-85) REVERT: D 274 ARG cc_start: 0.7300 (ptp-110) cc_final: 0.6935 (pmt170) REVERT: D 291 ARG cc_start: 0.7011 (mmm160) cc_final: 0.6510 (mtm110) REVERT: D 303 MET cc_start: 0.7002 (mtm) cc_final: 0.5887 (mmm) REVERT: D 433 GLN cc_start: 0.7341 (tt0) cc_final: 0.6986 (tt0) REVERT: D 442 LYS cc_start: 0.7486 (mmmt) cc_final: 0.6966 (tttm) REVERT: D 492 ARG cc_start: 0.8135 (ttp-110) cc_final: 0.7787 (ttp-110) REVERT: D 539 GLN cc_start: 0.7921 (pt0) cc_final: 0.7669 (pt0) REVERT: D 548 VAL cc_start: 0.5053 (OUTLIER) cc_final: 0.4697 (m) outliers start: 43 outliers final: 20 residues processed: 278 average time/residue: 1.4435 time to fit residues: 444.1859 Evaluate side-chains 259 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 548 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 10.0000 chunk 171 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 110 optimal weight: 0.0000 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18040 Z= 0.168 Angle : 0.518 15.185 24300 Z= 0.273 Chirality : 0.040 0.187 2624 Planarity : 0.004 0.054 2952 Dihedral : 12.332 121.735 2818 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.88 % Allowed : 19.09 % Favored : 79.03 % 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: 1.09 (0.18), residues: 2036 helix: 1.69 (0.15), residues: 1192 sheet: 2.23 (0.48), residues: 96 loop : -1.11 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 451 HIS 0.002 0.001 HIS A 321 PHE 0.019 0.001 PHE D 138 TYR 0.024 0.001 TYR D 434 ARG 0.012 0.000 ARG C 492 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 242 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7187 (ttp) cc_final: 0.6857 (mmt) REVERT: A 251 ARG cc_start: 0.7188 (mtt90) cc_final: 0.6800 (mtm-85) REVERT: A 274 ARG cc_start: 0.7377 (ptp-110) cc_final: 0.6974 (pmt170) REVERT: A 291 ARG cc_start: 0.7012 (mmm160) cc_final: 0.6527 (mtm110) REVERT: A 303 MET cc_start: 0.7005 (mtm) cc_final: 0.5949 (mmm) REVERT: A 433 GLN cc_start: 0.7369 (tt0) cc_final: 0.7097 (tt0) REVERT: A 442 LYS cc_start: 0.7474 (mmmt) cc_final: 0.6972 (tttm) REVERT: B 202 MET cc_start: 0.7190 (ttp) cc_final: 0.6847 (mmt) REVERT: B 251 ARG cc_start: 0.7073 (mtt90) cc_final: 0.6761 (mtm-85) REVERT: B 274 ARG cc_start: 0.7398 (ptp-110) cc_final: 0.6993 (pmt170) REVERT: B 291 ARG cc_start: 0.6967 (mmm160) cc_final: 0.6551 (mtm110) REVERT: B 303 MET cc_start: 0.6964 (mtm) cc_final: 0.5855 (mmm) REVERT: B 433 GLN cc_start: 0.7419 (tt0) cc_final: 0.7049 (tt0) REVERT: B 442 LYS cc_start: 0.7466 (mmmt) cc_final: 0.6959 (tttm) REVERT: B 443 GLN cc_start: 0.6735 (tm-30) cc_final: 0.6438 (tp40) REVERT: C 202 MET cc_start: 0.7153 (ttp) cc_final: 0.6813 (mmt) REVERT: C 211 MET cc_start: 0.8120 (mmt) cc_final: 0.7788 (mmm) REVERT: C 251 ARG cc_start: 0.7202 (mtt90) cc_final: 0.6776 (mtm-85) REVERT: C 274 ARG cc_start: 0.7377 (ptp-110) cc_final: 0.6941 (pmt170) REVERT: C 291 ARG cc_start: 0.7008 (mmm160) cc_final: 0.6525 (mtm110) REVERT: C 303 MET cc_start: 0.7008 (mtm) cc_final: 0.5952 (mmm) REVERT: C 428 MET cc_start: 0.6359 (mmm) cc_final: 0.6003 (mmt) REVERT: C 433 GLN cc_start: 0.7400 (tt0) cc_final: 0.7043 (tt0) REVERT: C 442 LYS cc_start: 0.7447 (mmmt) cc_final: 0.6880 (tttm) REVERT: C 539 GLN cc_start: 0.7981 (pt0) cc_final: 0.7771 (pt0) REVERT: C 606 ARG cc_start: 0.7392 (ttp-110) cc_final: 0.7151 (ttm110) REVERT: D 202 MET cc_start: 0.7187 (ttp) cc_final: 0.6844 (mmt) REVERT: D 251 ARG cc_start: 0.7190 (mtt90) cc_final: 0.6771 (mtm-85) REVERT: D 274 ARG cc_start: 0.7344 (ptp-110) cc_final: 0.6925 (pmt170) REVERT: D 291 ARG cc_start: 0.7007 (mmm160) cc_final: 0.6529 (mtm110) REVERT: D 303 MET cc_start: 0.6945 (mtm) cc_final: 0.5857 (mmm) REVERT: D 428 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6339 (mmt) REVERT: D 433 GLN cc_start: 0.7403 (tt0) cc_final: 0.7050 (tt0) REVERT: D 442 LYS cc_start: 0.7455 (mmmt) cc_final: 0.6901 (tttm) REVERT: D 452 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: D 537 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7464 (ttp-170) REVERT: D 539 GLN cc_start: 0.7884 (pt0) cc_final: 0.7626 (pt0) outliers start: 35 outliers final: 20 residues processed: 267 average time/residue: 1.4109 time to fit residues: 418.7186 Evaluate side-chains 259 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 515 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 553 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18040 Z= 0.260 Angle : 0.574 11.650 24300 Z= 0.300 Chirality : 0.042 0.203 2624 Planarity : 0.004 0.043 2952 Dihedral : 12.863 122.986 2818 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.08 % Allowed : 20.70 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2036 helix: 1.49 (0.14), residues: 1216 sheet: 2.11 (0.48), residues: 96 loop : -1.08 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 451 HIS 0.003 0.001 HIS C 321 PHE 0.019 0.002 PHE B 138 TYR 0.026 0.002 TYR B 434 ARG 0.009 0.000 ARG C 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 245 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7227 (ttp) cc_final: 0.6876 (mmt) REVERT: A 251 ARG cc_start: 0.7240 (mtt90) cc_final: 0.6844 (mtm-85) REVERT: A 274 ARG cc_start: 0.7410 (ptp-110) cc_final: 0.6995 (pmt170) REVERT: A 291 ARG cc_start: 0.7017 (mmm160) cc_final: 0.6529 (mtm110) REVERT: A 303 MET cc_start: 0.7059 (mtm) cc_final: 0.5933 (mmm) REVERT: A 428 MET cc_start: 0.6633 (mmm) cc_final: 0.6233 (mmt) REVERT: A 433 GLN cc_start: 0.7440 (tt0) cc_final: 0.7133 (tt0) REVERT: A 442 LYS cc_start: 0.7536 (mmmt) cc_final: 0.7021 (tttm) REVERT: B 202 MET cc_start: 0.7228 (ttp) cc_final: 0.6876 (mmt) REVERT: B 251 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6797 (mtm-85) REVERT: B 274 ARG cc_start: 0.7445 (ptp-110) cc_final: 0.7071 (pmt170) REVERT: B 303 MET cc_start: 0.7086 (mtm) cc_final: 0.5978 (mmm) REVERT: B 433 GLN cc_start: 0.7428 (tt0) cc_final: 0.7063 (tt0) REVERT: B 442 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7186 (tttm) REVERT: B 443 GLN cc_start: 0.6816 (tm-30) cc_final: 0.6527 (tp-100) REVERT: C 202 MET cc_start: 0.7226 (ttp) cc_final: 0.6878 (mmt) REVERT: C 251 ARG cc_start: 0.7213 (mtt90) cc_final: 0.6811 (mtm-85) REVERT: C 274 ARG cc_start: 0.7411 (ptp-110) cc_final: 0.6998 (pmt170) REVERT: C 291 ARG cc_start: 0.7014 (mmm160) cc_final: 0.6527 (mtm110) REVERT: C 303 MET cc_start: 0.7060 (mtm) cc_final: 0.5882 (mmm) REVERT: C 428 MET cc_start: 0.6623 (mmm) cc_final: 0.6307 (mmt) REVERT: C 433 GLN cc_start: 0.7400 (tt0) cc_final: 0.7038 (tt0) REVERT: C 442 LYS cc_start: 0.7556 (mmmt) cc_final: 0.7020 (tttm) REVERT: C 528 ARG cc_start: 0.6880 (ppt170) cc_final: 0.6537 (ppt170) REVERT: C 539 GLN cc_start: 0.8034 (pt0) cc_final: 0.7832 (pt0) REVERT: C 606 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.7202 (ttm110) REVERT: D 202 MET cc_start: 0.7228 (ttp) cc_final: 0.6877 (mmt) REVERT: D 251 ARG cc_start: 0.7243 (mtt90) cc_final: 0.6838 (mtm-85) REVERT: D 274 ARG cc_start: 0.7394 (ptp-110) cc_final: 0.6973 (pmt170) REVERT: D 291 ARG cc_start: 0.7013 (mmm160) cc_final: 0.6530 (mtm110) REVERT: D 303 MET cc_start: 0.7074 (mtm) cc_final: 0.5948 (mmm) REVERT: D 428 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.6353 (mmt) REVERT: D 433 GLN cc_start: 0.7407 (tt0) cc_final: 0.7046 (tt0) REVERT: D 442 LYS cc_start: 0.7532 (mmmt) cc_final: 0.6997 (tttm) REVERT: D 492 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7953 (ttp-110) REVERT: D 539 GLN cc_start: 0.7938 (pt0) cc_final: 0.7711 (pt0) REVERT: D 542 ASP cc_start: 0.7110 (m-30) cc_final: 0.6794 (p0) outliers start: 20 outliers final: 20 residues processed: 258 average time/residue: 1.4696 time to fit residues: 420.2690 Evaluate side-chains 262 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 241 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain D residue 515 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.173667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116118 restraints weight = 19620.944| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.93 r_work: 0.3387 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18040 Z= 0.232 Angle : 0.564 13.320 24300 Z= 0.294 Chirality : 0.042 0.173 2624 Planarity : 0.004 0.044 2952 Dihedral : 12.769 122.841 2818 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.34 % Allowed : 20.65 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.90 (0.18), residues: 2036 helix: 1.46 (0.14), residues: 1220 sheet: 2.08 (0.48), residues: 96 loop : -1.13 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 451 HIS 0.003 0.001 HIS B 321 PHE 0.017 0.002 PHE A 138 TYR 0.025 0.002 TYR C 434 ARG 0.009 0.000 ARG B 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7240.38 seconds wall clock time: 128 minutes 42.96 seconds (7722.96 seconds total)