Starting phenix.real_space_refine on Sun Mar 17 13:03:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n15_24113/03_2024/7n15_24113_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n15_24113/03_2024/7n15_24113.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n15_24113/03_2024/7n15_24113_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n15_24113/03_2024/7n15_24113_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n15_24113/03_2024/7n15_24113_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n15_24113/03_2024/7n15_24113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n15_24113/03_2024/7n15_24113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n15_24113/03_2024/7n15_24113_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n15_24113/03_2024/7n15_24113_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.180 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 96 5.16 5 C 11636 2.51 5 N 2904 2.21 5 O 3148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A ASP 496": "OD1" <-> "OD2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 353": "OD1" <-> "OD2" Residue "B TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B ASP 496": "OD1" <-> "OD2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 353": "OD1" <-> "OD2" Residue "C TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C ASP 496": "OD1" <-> "OD2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 353": "OD1" <-> "OD2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "D TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D ASP 496": "OD1" <-> "OD2" Residue "D ASP 518": "OD1" <-> "OD2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D ARG 580": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17800 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4295 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 15, 'TRANS': 504} Chain: "B" Number of atoms: 4295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4295 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 15, 'TRANS': 504} Chain: "C" Number of atoms: 4295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4295 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 15, 'TRANS': 504} Chain: "D" Number of atoms: 4295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4295 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 15, 'TRANS': 504} Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Unusual residues: {'CPL': 5, 'PCG': 1, 'PX2': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 5, 'CPL:plan-3': 5, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Unusual residues: {'CPL': 5, 'PCG': 1, 'PX2': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 5, 'CPL:plan-3': 5, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Unusual residues: {'CPL': 5, 'PCG': 1, 'PX2': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 5, 'CPL:plan-3': 5, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Unusual residues: {'CPL': 5, 'PCG': 1, 'PX2': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 5, 'CPL:plan-3': 5, 'CPL:plan-2': 3, 'CPL:plan-1': 3} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 9.54, per 1000 atoms: 0.54 Number of scatterers: 17800 At special positions: 0 Unit cell: (138.61, 138.61, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 16 15.00 O 3148 8.00 N 2904 7.00 C 11636 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=2.02 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 172 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 172 " distance=2.02 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 172 " distance=2.02 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: 6.47 Conformation dependent library (CDL) restraints added in 3.0 seconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 12 sheets defined 54.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 119 through 144 Processing helix chain 'A' and resid 146 through 149 removed outlier: 4.065A pdb=" N ILE A 149 " --> pdb=" O ASN A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 198 through 223 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.512A 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 280 removed outlier: 4.043A pdb=" N ARG A 280 " --> pdb=" O PRO A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 288 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 437 removed outlier: 3.551A pdb=" N MET A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 464 through 470 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 485 through 488 No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 492 through 495 No H-bonds generated for 'chain 'A' and resid 492 through 495' Processing helix chain 'A' and resid 499 through 507 removed outlier: 5.026A pdb=" N LEU A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 603 through 619 Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 119 through 144 Processing helix chain 'B' and resid 146 through 149 removed outlier: 4.065A pdb=" N ILE B 149 " --> pdb=" O ASN B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 237 through 245 Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.513A 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 280 removed outlier: 4.043A pdb=" N ARG B 280 " --> pdb=" O PRO B 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 280' Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 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 437 removed outlier: 3.551A pdb=" N MET B 417 " --> pdb=" O MET B 413 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 457 Processing helix chain 'B' and resid 464 through 470 Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 485 through 488 No H-bonds generated for 'chain 'B' and resid 485 through 488' Processing helix chain 'B' and resid 492 through 495 No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 499 through 507 removed outlier: 5.025A pdb=" N LEU B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 603 through 619 Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 119 through 144 Processing helix chain 'C' and resid 146 through 149 removed outlier: 4.066A pdb=" N ILE C 149 " --> pdb=" O ASN C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 198 through 223 Processing helix chain 'C' and resid 237 through 245 Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.512A 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 280 removed outlier: 4.043A pdb=" N ARG C 280 " --> pdb=" O PRO C 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 280' Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 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 437 removed outlier: 3.551A pdb=" N MET C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ALA C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP C 421 " --> pdb=" O MET C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 457 Processing helix chain 'C' and resid 464 through 470 Processing helix chain 'C' and resid 473 through 483 Processing helix chain 'C' and resid 485 through 488 No H-bonds generated for 'chain 'C' and resid 485 through 488' Processing helix chain 'C' and resid 492 through 495 No H-bonds generated for 'chain 'C' and resid 492 through 495' Processing helix chain 'C' and resid 499 through 507 removed outlier: 5.026A pdb=" N LEU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 601 Processing helix chain 'C' and resid 603 through 619 Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 119 through 144 Processing helix chain 'D' and resid 146 through 149 removed outlier: 4.065A pdb=" N ILE D 149 " --> pdb=" O ASN D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 198 through 223 Processing helix chain 'D' and resid 237 through 245 Processing helix chain 'D' and resid 249 through 257 removed outlier: 3.513A 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 280 removed outlier: 4.044A pdb=" N ARG D 280 " --> pdb=" O PRO D 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 277 through 280' Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 288 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 437 removed outlier: 3.551A pdb=" N MET D 417 " --> pdb=" O MET D 413 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 419 " --> pdb=" O SER D 415 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP D 421 " --> pdb=" O MET D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 457 Processing helix chain 'D' and resid 464 through 470 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 488 No H-bonds generated for 'chain 'D' and resid 485 through 488' Processing helix chain 'D' and resid 492 through 495 No H-bonds generated for 'chain 'D' and resid 492 through 495' Processing helix chain 'D' and resid 499 through 507 removed outlier: 5.026A pdb=" N LEU D 507 " --> pdb=" O ALA D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 601 Processing helix chain 'D' and resid 603 through 619 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 removed outlier: 6.002A pdb=" N PHE A 588 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL A 533 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 590 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR A 531 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 578 through 581 removed outlier: 3.832A pdb=" N ASN A 578 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 550 " --> pdb=" O VAL A 540 " (cutoff:3.500A) 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 removed outlier: 6.002A pdb=" N PHE B 588 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL B 533 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU B 590 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR B 531 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 578 through 581 removed outlier: 3.832A pdb=" N ASN B 578 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 550 " --> pdb=" O VAL B 540 " (cutoff:3.500A) 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 removed outlier: 6.002A pdb=" N PHE C 588 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL C 533 " --> pdb=" O PHE C 588 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU C 590 " --> pdb=" O TYR C 531 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR C 531 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 578 through 581 removed outlier: 3.832A pdb=" N ASN C 578 " --> pdb=" O VAL C 541 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 550 " --> pdb=" O VAL C 540 " (cutoff:3.500A) 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 removed outlier: 6.003A pdb=" N PHE D 588 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL D 533 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU D 590 " --> pdb=" O TYR D 531 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR D 531 " --> pdb=" O LEU D 590 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 578 through 581 removed outlier: 3.832A pdb=" N ASN D 578 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL D 550 " --> pdb=" O VAL D 540 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2696 1.31 - 1.43: 5150 1.43 - 1.56: 10178 1.56 - 1.68: 32 1.68 - 1.81: 156 Bond restraints: 18212 Sorted by residual: bond pdb=" C3' PCG C 801 " pdb=" C4' PCG C 801 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C3' PCG D 801 " pdb=" C4' PCG D 801 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C3' PCG A 801 " pdb=" C4' PCG A 801 " ideal model delta sigma weight residual 1.808 1.496 0.312 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C3' PCG B 801 " pdb=" C4' PCG B 801 " ideal model delta sigma weight residual 1.808 1.496 0.312 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C2' PCG C 801 " pdb=" C3' PCG C 801 " ideal model delta sigma weight residual 1.200 1.495 -0.295 2.00e-02 2.50e+03 2.17e+02 ... (remaining 18207 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.80: 292 105.80 - 112.92: 9683 112.92 - 120.04: 6939 120.04 - 127.17: 7458 127.17 - 134.29: 248 Bond angle restraints: 24620 Sorted by residual: angle pdb=" N ALA C 110 " pdb=" CA ALA C 110 " pdb=" C ALA C 110 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 angle pdb=" N ALA D 110 " pdb=" CA ALA D 110 " pdb=" C ALA D 110 " ideal model delta sigma weight residual 111.36 118.93 -7.57 1.09e+00 8.42e-01 4.82e+01 angle pdb=" N ALA A 110 " pdb=" CA ALA A 110 " pdb=" C ALA A 110 " ideal model delta sigma weight residual 111.36 118.93 -7.57 1.09e+00 8.42e-01 4.82e+01 angle pdb=" N ALA B 110 " pdb=" CA ALA B 110 " pdb=" C ALA B 110 " ideal model delta sigma weight residual 111.36 118.92 -7.56 1.09e+00 8.42e-01 4.81e+01 angle pdb=" N TYR B 112 " pdb=" CA TYR B 112 " pdb=" C TYR B 112 " ideal model delta sigma weight residual 109.76 98.76 11.00 1.64e+00 3.72e-01 4.50e+01 ... (remaining 24615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 10492 35.90 - 71.80: 296 71.80 - 107.70: 20 107.70 - 143.60: 4 143.60 - 179.49: 16 Dihedral angle restraints: 10828 sinusoidal: 4688 harmonic: 6140 Sorted by residual: dihedral pdb=" C3 CPL D 802 " pdb=" C1 CPL D 802 " pdb=" C2 CPL D 802 " pdb=" O3P CPL D 802 " ideal model delta sinusoidal sigma weight residual 72.09 -107.40 179.49 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C2 CPL B 802 " pdb=" O3P CPL B 802 " ideal model delta sinusoidal sigma weight residual 72.09 -107.39 179.48 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL C 802 " pdb=" C1 CPL C 802 " pdb=" C2 CPL C 802 " pdb=" O3P CPL C 802 " ideal model delta sinusoidal sigma weight residual 72.09 -107.38 179.47 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2403 0.095 - 0.190: 233 0.190 - 0.284: 24 0.284 - 0.379: 12 0.379 - 0.474: 4 Chirality restraints: 2676 Sorted by residual: chirality pdb=" C3' PCG B 801 " pdb=" C2' PCG B 801 " pdb=" C4' PCG B 801 " pdb=" O3' PCG B 801 " both_signs ideal model delta sigma weight residual False -2.10 -2.58 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" C3' PCG A 801 " pdb=" C2' PCG A 801 " pdb=" C4' PCG A 801 " pdb=" O3' PCG A 801 " both_signs ideal model delta sigma weight residual False -2.10 -2.58 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" C3' PCG C 801 " pdb=" C2' PCG C 801 " pdb=" C4' PCG C 801 " pdb=" O3' PCG C 801 " both_signs ideal model delta sigma weight residual False -2.10 -2.57 0.47 2.00e-01 2.50e+01 5.57e+00 ... (remaining 2673 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 150 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO C 151 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 150 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.33e+00 pdb=" N PRO A 151 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 150 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO B 151 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 151 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 151 " -0.042 5.00e-02 4.00e+02 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1425 2.74 - 3.28: 16291 3.28 - 3.82: 30204 3.82 - 4.36: 37443 4.36 - 4.90: 63627 Nonbonded interactions: 148990 Sorted by model distance: nonbonded pdb=" O ASN B 111 " pdb=" OD1 ASN B 111 " model vdw 2.199 3.040 nonbonded pdb=" O ASN A 111 " pdb=" OD1 ASN A 111 " model vdw 2.199 3.040 nonbonded pdb=" O ASN D 111 " pdb=" OD1 ASN D 111 " model vdw 2.199 3.040 nonbonded pdb=" O ASN C 111 " pdb=" OD1 ASN C 111 " model vdw 2.199 3.040 nonbonded pdb=" OG SER C 581 " pdb=" O GLY C 583 " model vdw 2.323 2.440 ... (remaining 148985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 1.560 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: 0.020 Extract box with map and model: 6.530 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 46.700 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.013 0.313 18212 Z= 0.819 Angle : 1.153 16.052 24620 Z= 0.600 Chirality : 0.064 0.474 2676 Planarity : 0.008 0.076 2984 Dihedral : 17.688 179.494 6880 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.43 % Allowed : 4.89 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.15), residues: 2072 helix: -2.56 (0.10), residues: 1184 sheet: -1.90 (0.38), residues: 96 loop : -0.94 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 124 HIS 0.005 0.002 HIS C 199 PHE 0.024 0.003 PHE D 138 TYR 0.020 0.003 TYR C 343 ARG 0.005 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 375 time to evaluate : 2.137 Fit side-chains revert: symmetry clash REVERT: A 438 ARG cc_start: 0.8230 (mpt180) cc_final: 0.8019 (mmt-90) REVERT: B 438 ARG cc_start: 0.8241 (mpt180) cc_final: 0.8017 (mmt-90) REVERT: C 438 ARG cc_start: 0.8238 (mpt180) cc_final: 0.8015 (mmt-90) REVERT: D 438 ARG cc_start: 0.8256 (mpt180) cc_final: 0.8030 (mmt-90) outliers start: 8 outliers final: 4 residues processed: 379 average time/residue: 1.3798 time to fit residues: 579.1090 Evaluate side-chains 270 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 266 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 199 HIS A 230 GLN A 416 ASN A 458 ASN A 565 ASN B 179 ASN B 199 HIS B 230 GLN B 246 GLN B 458 ASN B 565 ASN C 179 ASN C 199 HIS C 230 GLN C 458 ASN C 565 ASN D 179 ASN D 199 HIS D 458 ASN D 565 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18212 Z= 0.247 Angle : 0.534 10.445 24620 Z= 0.280 Chirality : 0.041 0.147 2676 Planarity : 0.005 0.057 2984 Dihedral : 17.075 171.202 2776 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.29 % Allowed : 11.86 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2072 helix: -0.75 (0.13), residues: 1252 sheet: -0.78 (0.43), residues: 88 loop : -0.36 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 596 HIS 0.005 0.002 HIS B 321 PHE 0.017 0.002 PHE B 138 TYR 0.015 0.001 TYR A 363 ARG 0.009 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 299 time to evaluate : 2.002 Fit side-chains REVERT: A 158 ARG cc_start: 0.7336 (mtt-85) cc_final: 0.7097 (mtt-85) REVERT: A 242 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7638 (tttp) REVERT: A 250 TYR cc_start: 0.7876 (p90) cc_final: 0.7600 (p90) REVERT: A 504 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: B 242 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7651 (tttp) REVERT: B 250 TYR cc_start: 0.7851 (p90) cc_final: 0.7538 (p90) REVERT: B 438 ARG cc_start: 0.8294 (mpt180) cc_final: 0.8026 (mmt-90) REVERT: B 504 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7175 (tp30) REVERT: C 242 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7669 (tttp) REVERT: C 248 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7530 (mmtm) REVERT: C 250 TYR cc_start: 0.7850 (p90) cc_final: 0.7497 (p90) REVERT: C 438 ARG cc_start: 0.8286 (mpt180) cc_final: 0.8038 (mmt-90) REVERT: C 504 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: D 242 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7673 (tttp) REVERT: D 248 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7539 (mmtm) REVERT: D 250 TYR cc_start: 0.7880 (p90) cc_final: 0.7611 (p90) REVERT: D 504 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7408 (tt0) outliers start: 43 outliers final: 17 residues processed: 318 average time/residue: 1.3484 time to fit residues: 475.2101 Evaluate side-chains 279 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 258 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 594 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 189 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN C 246 GLN C 416 ASN D 246 GLN D 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18212 Z= 0.284 Angle : 0.550 11.425 24620 Z= 0.281 Chirality : 0.042 0.153 2676 Planarity : 0.004 0.054 2984 Dihedral : 16.284 166.561 2776 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.09 % Allowed : 13.46 % Favored : 83.46 % 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: -0.28 (0.18), residues: 2072 helix: -0.00 (0.14), residues: 1248 sheet: -0.38 (0.42), residues: 96 loop : -0.19 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 596 HIS 0.004 0.002 HIS C 321 PHE 0.020 0.002 PHE C 138 TYR 0.014 0.001 TYR C 363 ARG 0.006 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 266 time to evaluate : 1.897 Fit side-chains REVERT: A 236 GLU cc_start: 0.6605 (pm20) cc_final: 0.6365 (mp0) REVERT: A 242 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7626 (tttp) REVERT: A 250 TYR cc_start: 0.7905 (p90) cc_final: 0.7619 (p90) REVERT: A 504 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: B 236 GLU cc_start: 0.6597 (pm20) cc_final: 0.6328 (mp0) REVERT: B 242 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7670 (tttp) REVERT: B 250 TYR cc_start: 0.7882 (p90) cc_final: 0.7590 (p90) REVERT: B 504 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: C 236 GLU cc_start: 0.6605 (pm20) cc_final: 0.6339 (mp0) REVERT: C 242 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7681 (tttp) REVERT: C 250 TYR cc_start: 0.7839 (p90) cc_final: 0.7515 (p90) REVERT: C 504 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: D 242 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7701 (tttp) REVERT: D 250 TYR cc_start: 0.7881 (p90) cc_final: 0.7580 (p90) REVERT: D 504 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7406 (tt0) outliers start: 58 outliers final: 26 residues processed: 287 average time/residue: 1.3445 time to fit residues: 429.4469 Evaluate side-chains 294 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 264 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 591 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN B 169 GLN C 169 GLN D 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18212 Z= 0.155 Angle : 0.456 8.588 24620 Z= 0.239 Chirality : 0.039 0.136 2676 Planarity : 0.003 0.046 2984 Dihedral : 15.401 164.458 2776 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.46 % Allowed : 14.31 % Favored : 82.23 % 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: 0.40 (0.18), residues: 2072 helix: 0.57 (0.15), residues: 1248 sheet: -0.07 (0.41), residues: 96 loop : 0.02 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 596 HIS 0.003 0.001 HIS C 321 PHE 0.017 0.001 PHE A 138 TYR 0.010 0.001 TYR A 363 ARG 0.009 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 276 time to evaluate : 1.988 Fit side-chains REVERT: A 242 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7586 (tttp) REVERT: A 250 TYR cc_start: 0.7856 (p90) cc_final: 0.7531 (p90) REVERT: A 326 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 242 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7576 (tttp) REVERT: B 250 TYR cc_start: 0.7871 (p90) cc_final: 0.7553 (p90) REVERT: B 326 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8169 (mp) REVERT: B 504 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7360 (tp30) REVERT: C 242 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7611 (tttp) REVERT: C 250 TYR cc_start: 0.7812 (p90) cc_final: 0.7491 (p90) REVERT: D 242 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7593 (tttp) REVERT: D 250 TYR cc_start: 0.7868 (p90) cc_final: 0.7545 (p90) REVERT: D 326 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8170 (mp) outliers start: 65 outliers final: 23 residues processed: 295 average time/residue: 1.3189 time to fit residues: 434.1172 Evaluate side-chains 294 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 267 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 608 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 GLN D 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18212 Z= 0.166 Angle : 0.465 8.725 24620 Z= 0.242 Chirality : 0.039 0.133 2676 Planarity : 0.003 0.044 2984 Dihedral : 14.813 159.596 2776 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.09 % Allowed : 15.48 % Favored : 81.44 % 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: 0.73 (0.18), residues: 2072 helix: 0.81 (0.15), residues: 1256 sheet: 0.16 (0.40), residues: 96 loop : 0.19 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 596 HIS 0.003 0.001 HIS A 321 PHE 0.018 0.001 PHE B 138 TYR 0.010 0.001 TYR A 363 ARG 0.009 0.000 ARG D 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 266 time to evaluate : 2.038 Fit side-chains REVERT: A 242 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7583 (tttp) REVERT: A 250 TYR cc_start: 0.7869 (p90) cc_final: 0.7536 (p90) REVERT: A 504 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: B 242 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7557 (tttp) REVERT: B 250 TYR cc_start: 0.7859 (p90) cc_final: 0.7529 (p90) REVERT: B 326 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8133 (mp) REVERT: B 504 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: B 610 LEU cc_start: 0.8493 (mp) cc_final: 0.7945 (mp) REVERT: C 242 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7590 (tttp) REVERT: C 250 TYR cc_start: 0.7806 (p90) cc_final: 0.7482 (p90) REVERT: C 504 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7297 (tp30) REVERT: D 242 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7593 (tttp) REVERT: D 250 TYR cc_start: 0.7871 (p90) cc_final: 0.7575 (p90) REVERT: D 504 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: D 608 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8117 (mt) REVERT: D 610 LEU cc_start: 0.8492 (mp) cc_final: 0.7955 (mp) outliers start: 58 outliers final: 31 residues processed: 286 average time/residue: 1.3434 time to fit residues: 428.1076 Evaluate side-chains 301 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 264 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 608 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 16 optimal weight: 0.0980 chunk 66 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN C 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18212 Z= 0.170 Angle : 0.463 8.830 24620 Z= 0.241 Chirality : 0.039 0.135 2676 Planarity : 0.003 0.043 2984 Dihedral : 14.454 155.071 2776 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.67 % Allowed : 15.21 % Favored : 81.12 % 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: 0.85 (0.18), residues: 2072 helix: 0.90 (0.15), residues: 1256 sheet: 0.30 (0.40), residues: 96 loop : 0.24 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 596 HIS 0.003 0.001 HIS C 321 PHE 0.018 0.001 PHE B 138 TYR 0.011 0.001 TYR D 363 ARG 0.007 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 271 time to evaluate : 1.844 Fit side-chains REVERT: A 235 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7399 (mmm160) REVERT: A 242 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7587 (tttp) REVERT: A 250 TYR cc_start: 0.7883 (p90) cc_final: 0.7582 (p90) REVERT: A 504 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: A 610 LEU cc_start: 0.8491 (mp) cc_final: 0.7931 (mp) REVERT: B 242 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7630 (tttp) REVERT: B 250 TYR cc_start: 0.7873 (p90) cc_final: 0.7544 (p90) REVERT: B 504 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: B 610 LEU cc_start: 0.8493 (mp) cc_final: 0.7970 (mp) REVERT: C 242 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7615 (tttp) REVERT: C 250 TYR cc_start: 0.7833 (p90) cc_final: 0.7508 (p90) REVERT: C 504 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7296 (tp30) REVERT: C 610 LEU cc_start: 0.8486 (mp) cc_final: 0.7959 (mp) REVERT: D 242 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7654 (tttm) REVERT: D 250 TYR cc_start: 0.7883 (p90) cc_final: 0.7560 (p90) REVERT: D 504 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7225 (tp30) REVERT: D 610 LEU cc_start: 0.8483 (mp) cc_final: 0.7959 (mp) outliers start: 69 outliers final: 33 residues processed: 302 average time/residue: 1.3016 time to fit residues: 437.7608 Evaluate side-chains 305 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 267 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 591 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 146 optimal weight: 0.0060 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN D 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18212 Z= 0.272 Angle : 0.545 11.135 24620 Z= 0.276 Chirality : 0.042 0.160 2676 Planarity : 0.004 0.046 2984 Dihedral : 14.737 150.284 2776 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.19 % Allowed : 16.22 % Favored : 80.59 % 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: 0.70 (0.18), residues: 2072 helix: 0.75 (0.15), residues: 1256 sheet: 0.59 (0.38), residues: 96 loop : 0.18 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 596 HIS 0.004 0.002 HIS C 321 PHE 0.018 0.002 PHE D 138 TYR 0.013 0.001 TYR B 363 ARG 0.006 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 268 time to evaluate : 2.010 Fit side-chains REVERT: A 235 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7971 (mmm160) REVERT: A 242 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7598 (tttm) REVERT: A 250 TYR cc_start: 0.7953 (p90) cc_final: 0.7650 (p90) REVERT: A 504 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: A 610 LEU cc_start: 0.8521 (mp) cc_final: 0.7926 (mp) REVERT: B 242 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7843 (tttm) REVERT: B 250 TYR cc_start: 0.7930 (p90) cc_final: 0.7639 (p90) REVERT: B 439 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8070 (mtmt) REVERT: B 504 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7238 (tp30) REVERT: B 610 LEU cc_start: 0.8521 (mp) cc_final: 0.7931 (mp) REVERT: C 242 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7648 (tttm) REVERT: C 250 TYR cc_start: 0.7851 (p90) cc_final: 0.7571 (p90) REVERT: C 439 LYS cc_start: 0.8532 (mmtm) cc_final: 0.8062 (mtmt) REVERT: C 504 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7312 (tp30) REVERT: C 610 LEU cc_start: 0.8516 (mp) cc_final: 0.7966 (mp) REVERT: D 242 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7838 (tttm) REVERT: D 250 TYR cc_start: 0.7943 (p90) cc_final: 0.7627 (p90) REVERT: D 504 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: D 610 LEU cc_start: 0.8515 (mp) cc_final: 0.7930 (mp) outliers start: 60 outliers final: 31 residues processed: 297 average time/residue: 1.3301 time to fit residues: 439.8196 Evaluate side-chains 302 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 266 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 591 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN B 495 GLN C 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18212 Z= 0.145 Angle : 0.473 9.217 24620 Z= 0.243 Chirality : 0.039 0.133 2676 Planarity : 0.003 0.044 2984 Dihedral : 14.181 148.204 2776 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.77 % Allowed : 16.86 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2072 helix: 0.97 (0.15), residues: 1256 sheet: 0.61 (0.38), residues: 96 loop : 0.27 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 596 HIS 0.003 0.001 HIS B 321 PHE 0.017 0.001 PHE D 138 TYR 0.010 0.001 TYR B 365 ARG 0.007 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 275 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8486 (mmm-85) REVERT: A 242 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7574 (tttp) REVERT: A 250 TYR cc_start: 0.7920 (p90) cc_final: 0.7581 (p90) REVERT: A 326 LEU cc_start: 0.8329 (mp) cc_final: 0.8007 (mp) REVERT: A 504 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: B 242 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7788 (tttm) REVERT: B 250 TYR cc_start: 0.7900 (p90) cc_final: 0.7563 (p90) REVERT: B 326 LEU cc_start: 0.8344 (mp) cc_final: 0.8035 (mp) REVERT: B 439 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8058 (mtmt) REVERT: B 504 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: C 242 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7615 (tttp) REVERT: C 250 TYR cc_start: 0.7818 (p90) cc_final: 0.7516 (p90) REVERT: C 439 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8050 (mtmt) REVERT: C 504 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: D 242 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7799 (tttm) REVERT: D 250 TYR cc_start: 0.7875 (p90) cc_final: 0.7568 (p90) REVERT: D 326 LEU cc_start: 0.8336 (mp) cc_final: 0.8010 (mp) REVERT: D 504 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7241 (tp30) outliers start: 52 outliers final: 27 residues processed: 296 average time/residue: 1.3340 time to fit residues: 440.2058 Evaluate side-chains 300 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 268 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 591 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18212 Z= 0.194 Angle : 0.505 10.783 24620 Z= 0.258 Chirality : 0.040 0.160 2676 Planarity : 0.003 0.044 2984 Dihedral : 14.029 143.990 2776 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.03 % Allowed : 17.13 % Favored : 79.84 % 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: 1.11 (0.18), residues: 2072 helix: 1.10 (0.15), residues: 1232 sheet: 0.75 (0.40), residues: 96 loop : 0.32 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 596 HIS 0.004 0.001 HIS D 321 PHE 0.018 0.001 PHE D 138 TYR 0.011 0.001 TYR C 244 ARG 0.010 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 272 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8497 (mmm-85) REVERT: A 242 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7762 (tttm) REVERT: A 250 TYR cc_start: 0.7902 (p90) cc_final: 0.7590 (p90) REVERT: A 255 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8315 (mm) REVERT: A 504 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: B 242 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7797 (tttm) REVERT: B 250 TYR cc_start: 0.7911 (p90) cc_final: 0.7569 (p90) REVERT: B 439 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8061 (mtmt) REVERT: B 504 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: C 242 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7805 (tttm) REVERT: C 250 TYR cc_start: 0.7869 (p90) cc_final: 0.7560 (p90) REVERT: C 439 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8057 (mtmt) REVERT: C 504 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7280 (tp30) REVERT: D 242 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7831 (tttm) REVERT: D 250 TYR cc_start: 0.7941 (p90) cc_final: 0.7622 (p90) REVERT: D 439 LYS cc_start: 0.8561 (mmtm) cc_final: 0.7934 (mtmt) REVERT: D 504 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7242 (tp30) outliers start: 57 outliers final: 33 residues processed: 300 average time/residue: 1.3134 time to fit residues: 438.5915 Evaluate side-chains 309 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 270 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 591 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 127 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 chunk 131 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN D 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18212 Z= 0.147 Angle : 0.484 11.776 24620 Z= 0.245 Chirality : 0.039 0.145 2676 Planarity : 0.003 0.044 2984 Dihedral : 13.527 140.474 2774 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.02 % Allowed : 18.03 % Favored : 79.95 % 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: 1.27 (0.18), residues: 2072 helix: 1.23 (0.15), residues: 1232 sheet: 0.82 (0.41), residues: 96 loop : 0.38 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 596 HIS 0.003 0.001 HIS B 321 PHE 0.016 0.001 PHE A 138 TYR 0.010 0.001 TYR C 365 ARG 0.010 0.000 ARG C 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 279 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7712 (tttm) REVERT: A 250 TYR cc_start: 0.7869 (p90) cc_final: 0.7541 (p90) REVERT: A 439 LYS cc_start: 0.8473 (mmtm) cc_final: 0.8001 (mtmt) REVERT: A 504 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: A 512 GLN cc_start: 0.7831 (pt0) cc_final: 0.7572 (pt0) REVERT: B 242 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7807 (tttm) REVERT: B 250 TYR cc_start: 0.7881 (p90) cc_final: 0.7557 (p90) REVERT: B 326 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8065 (mp) REVERT: B 439 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8069 (mtmt) REVERT: B 495 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7292 (mm110) REVERT: B 504 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: C 242 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7738 (tttm) REVERT: C 250 TYR cc_start: 0.7829 (p90) cc_final: 0.7530 (p90) REVERT: C 439 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8066 (mtmt) REVERT: C 504 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: C 512 GLN cc_start: 0.7674 (pt0) cc_final: 0.7273 (pt0) REVERT: D 242 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7792 (tttm) REVERT: D 250 TYR cc_start: 0.7868 (p90) cc_final: 0.7524 (p90) REVERT: D 439 LYS cc_start: 0.8543 (mmtm) cc_final: 0.7936 (mtmt) REVERT: D 504 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7177 (tp30) REVERT: D 512 GLN cc_start: 0.7655 (pt0) cc_final: 0.7292 (pt0) outliers start: 38 outliers final: 19 residues processed: 294 average time/residue: 1.3097 time to fit residues: 430.2995 Evaluate side-chains 295 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 271 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 69 optimal weight: 0.0770 chunk 169 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.143540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107456 restraints weight = 18553.303| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.20 r_work: 0.2774 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18212 Z= 0.225 Angle : 0.534 12.997 24620 Z= 0.269 Chirality : 0.041 0.142 2676 Planarity : 0.004 0.045 2984 Dihedral : 13.712 137.731 2774 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.91 % Allowed : 17.98 % Favored : 80.11 % 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: 1.11 (0.18), residues: 2072 helix: 1.04 (0.15), residues: 1240 sheet: 0.93 (0.41), residues: 96 loop : 0.38 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 124 HIS 0.004 0.002 HIS C 321 PHE 0.019 0.001 PHE D 138 TYR 0.011 0.001 TYR C 363 ARG 0.010 0.000 ARG C 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7285.16 seconds wall clock time: 129 minutes 30.23 seconds (7770.23 seconds total)