Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 06:55:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2023/5h3o_6656_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2023/5h3o_6656.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2023/5h3o_6656_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2023/5h3o_6656_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2023/5h3o_6656_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2023/5h3o_6656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2023/5h3o_6656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2023/5h3o_6656_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2023/5h3o_6656_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 96 5.16 5 Na 3 4.78 5 C 11008 2.51 5 N 2852 2.21 5 O 2995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 473": "OD1" <-> "OD2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 473": "OD1" <-> "OD2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 601": "OE1" <-> "OE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 473": "OD1" <-> "OD2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 473": "OD1" <-> "OD2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 518": "OD1" <-> "OD2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 601": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16958 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4215 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4216 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Chain: "C" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4216 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Chain: "D" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4216 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' NA': 2, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' NA': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.97, per 1000 atoms: 0.53 Number of scatterers: 16958 At special positions: 0 Unit cell: (109.56, 109.56, 135.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 4 15.00 Na 3 11.00 O 2995 8.00 N 2852 7.00 C 11008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.23 Conformation dependent library (CDL) restraints added in 2.5 seconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 8 sheets defined 54.3% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 119 through 144 removed outlier: 5.415A pdb=" N ILE A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 223 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.500A pdb=" N LEU A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 277 through 298 removed outlier: 3.531A pdb=" N ILE A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 286 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS A 288 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A 295 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 298 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 333 removed outlier: 3.675A pdb=" N VAL A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 375 Processing helix chain 'A' and resid 386 through 416 removed outlier: 3.987A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 437 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 485 through 490 removed outlier: 3.738A pdb=" N LYS A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 502 through 508 removed outlier: 4.733A pdb=" N LEU A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 563 No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 603 through 618 removed outlier: 3.818A pdb=" N GLU A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 119 through 144 removed outlier: 5.404A pdb=" N ILE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 248 through 258 removed outlier: 4.223A pdb=" N ILE B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 277 through 298 removed outlier: 3.549A pdb=" N ILE B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR B 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS B 288 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU B 295 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 298 " --> pdb=" O GLU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 333 removed outlier: 3.664A pdb=" N VAL B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 375 Processing helix chain 'B' and resid 386 through 416 removed outlier: 3.995A pdb=" N ALA B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 437 Processing helix chain 'B' and resid 442 through 457 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 485 through 490 removed outlier: 3.741A pdb=" N LYS B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 502 through 508 removed outlier: 4.719A pdb=" N LEU B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 563 No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 603 through 618 removed outlier: 3.801A pdb=" N GLU B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 119 through 144 removed outlier: 5.395A pdb=" N ILE C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 223 Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 248 through 258 removed outlier: 4.221A pdb=" N ILE C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 277 through 298 removed outlier: 3.539A pdb=" N ILE C 285 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 286 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C 287 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS C 288 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU C 295 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 298 " --> pdb=" O GLU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 333 removed outlier: 3.662A pdb=" N VAL C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 375 Processing helix chain 'C' and resid 386 through 416 removed outlier: 3.999A pdb=" N ALA C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 437 Processing helix chain 'C' and resid 442 through 457 Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 473 through 483 Processing helix chain 'C' and resid 485 through 490 removed outlier: 3.733A pdb=" N LYS C 490 " --> pdb=" O GLU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 502 through 508 removed outlier: 4.694A pdb=" N LEU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 563 No H-bonds generated for 'chain 'C' and resid 560 through 563' Processing helix chain 'C' and resid 592 through 599 Processing helix chain 'C' and resid 603 through 618 removed outlier: 3.826A pdb=" N GLU C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 119 through 144 removed outlier: 5.429A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 223 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 248 through 258 removed outlier: 4.226A pdb=" N ILE D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 277 through 298 removed outlier: 3.527A pdb=" N ILE D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 286 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR D 287 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS D 288 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU D 295 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 298 " --> pdb=" O GLU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 333 removed outlier: 3.674A pdb=" N VAL D 312 " --> pdb=" O ARG D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 375 Processing helix chain 'D' and resid 386 through 416 removed outlier: 4.005A pdb=" N ALA D 404 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 437 Processing helix chain 'D' and resid 442 through 457 Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 490 removed outlier: 3.725A pdb=" N LYS D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 502 through 508 removed outlier: 4.730A pdb=" N LEU D 507 " --> pdb=" O ALA D 503 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS D 508 " --> pdb=" O GLU D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 563 No H-bonds generated for 'chain 'D' and resid 560 through 563' Processing helix chain 'D' and resid 592 through 599 Processing helix chain 'D' and resid 603 through 618 removed outlier: 3.794A pdb=" N GLU D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 510 through 514 removed outlier: 6.138A pdb=" N PHE A 588 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL A 533 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU A 590 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N TYR A 531 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 550 through 552 removed outlier: 4.136A pdb=" N ASN A 578 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 510 through 514 removed outlier: 6.125A pdb=" N PHE B 588 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL B 533 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 590 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N TYR B 531 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 550 through 552 removed outlier: 4.166A pdb=" N ASN B 578 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 510 through 514 removed outlier: 6.129A pdb=" N PHE C 588 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL C 533 " --> pdb=" O PHE C 588 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU C 590 " --> pdb=" O TYR C 531 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR C 531 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 550 through 552 removed outlier: 4.142A pdb=" N ASN C 578 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 510 through 514 removed outlier: 6.126A pdb=" N PHE D 588 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL D 533 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU D 590 " --> pdb=" O TYR D 531 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N TYR D 531 " --> pdb=" O LEU D 590 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 550 through 552 removed outlier: 4.140A pdb=" N ASN D 578 " --> pdb=" O VAL D 541 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2157 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: 4.59 Time building geometry restraints manager: 7.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4780 1.33 - 1.46: 3786 1.46 - 1.58: 8635 1.58 - 1.70: 18 1.70 - 1.83: 156 Bond restraints: 17375 Sorted by residual: bond pdb=" C3' PCG C 801 " pdb=" C4' PCG C 801 " ideal model delta sigma weight residual 1.808 1.499 0.309 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C3' PCG D 801 " pdb=" C4' PCG D 801 " ideal model delta sigma weight residual 1.808 1.500 0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C3' PCG A 801 " pdb=" C4' PCG A 801 " ideal model delta sigma weight residual 1.808 1.500 0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C3' PCG B 801 " pdb=" C4' PCG B 801 " ideal model delta sigma weight residual 1.808 1.501 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C2' PCG C 801 " pdb=" C3' PCG C 801 " ideal model delta sigma weight residual 1.200 1.496 -0.296 2.00e-02 2.50e+03 2.20e+02 ... (remaining 17370 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.85: 350 105.85 - 113.51: 9469 113.51 - 121.17: 8811 121.17 - 128.83: 4777 128.83 - 136.49: 179 Bond angle restraints: 23586 Sorted by residual: angle pdb=" N SER A 155 " pdb=" CA SER A 155 " pdb=" C SER A 155 " ideal model delta sigma weight residual 111.28 121.73 -10.45 1.09e+00 8.42e-01 9.20e+01 angle pdb=" N SER C 155 " pdb=" CA SER C 155 " pdb=" C SER C 155 " ideal model delta sigma weight residual 111.28 121.69 -10.41 1.09e+00 8.42e-01 9.12e+01 angle pdb=" N SER B 155 " pdb=" CA SER B 155 " pdb=" C SER B 155 " ideal model delta sigma weight residual 111.28 121.65 -10.37 1.09e+00 8.42e-01 9.05e+01 angle pdb=" N SER D 155 " pdb=" CA SER D 155 " pdb=" C SER D 155 " ideal model delta sigma weight residual 111.28 121.61 -10.33 1.09e+00 8.42e-01 8.99e+01 angle pdb=" N ILE B 377 " pdb=" CA ILE B 377 " pdb=" C ILE B 377 " ideal model delta sigma weight residual 111.45 102.65 8.80 9.30e-01 1.16e+00 8.96e+01 ... (remaining 23581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 8988 17.73 - 35.46: 899 35.46 - 53.19: 250 53.19 - 70.92: 58 70.92 - 88.64: 20 Dihedral angle restraints: 10215 sinusoidal: 4196 harmonic: 6019 Sorted by residual: dihedral pdb=" C LEU A 346 " pdb=" N LEU A 346 " pdb=" CA LEU A 346 " pdb=" CB LEU A 346 " ideal model delta harmonic sigma weight residual -122.60 -152.85 30.25 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" N LEU A 346 " pdb=" C LEU A 346 " pdb=" CA LEU A 346 " pdb=" CB LEU A 346 " ideal model delta harmonic sigma weight residual 122.80 151.82 -29.02 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" C LEU D 346 " pdb=" N LEU D 346 " pdb=" CA LEU D 346 " pdb=" CB LEU D 346 " ideal model delta harmonic sigma weight residual -122.60 -151.48 28.88 0 2.50e+00 1.60e-01 1.33e+02 ... (remaining 10212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 2592 0.261 - 0.523: 16 0.523 - 0.784: 0 0.784 - 1.046: 0 1.046 - 1.307: 4 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CA LEU A 346 " pdb=" N LEU A 346 " pdb=" C LEU A 346 " pdb=" CB LEU A 346 " both_signs ideal model delta sigma weight residual False 2.51 1.20 1.31 2.00e-01 2.50e+01 4.27e+01 chirality pdb=" CA LEU D 346 " pdb=" N LEU D 346 " pdb=" C LEU D 346 " pdb=" CB LEU D 346 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.94e+01 chirality pdb=" CA LEU B 346 " pdb=" N LEU B 346 " pdb=" C LEU B 346 " pdb=" CB LEU B 346 " both_signs ideal model delta sigma weight residual False 2.51 1.29 1.22 2.00e-01 2.50e+01 3.70e+01 ... (remaining 2609 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 347 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASN D 347 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN D 347 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS D 348 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 347 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C ASN A 347 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 347 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 348 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 347 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C ASN C 347 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN C 347 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS C 348 " -0.014 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2881 2.77 - 3.30: 18081 3.30 - 3.83: 27385 3.83 - 4.37: 33820 4.37 - 4.90: 54043 Nonbonded interactions: 136210 Sorted by model distance: nonbonded pdb=" O GLY A 572 " pdb=" N ARG A 574 " model vdw 2.235 2.520 nonbonded pdb=" O GLY B 572 " pdb=" N ARG B 574 " model vdw 2.236 2.520 nonbonded pdb=" O GLY C 572 " pdb=" N ARG C 574 " model vdw 2.239 2.520 nonbonded pdb=" O GLY D 572 " pdb=" N ARG D 574 " model vdw 2.239 2.520 nonbonded pdb=" NH2 ARG A 537 " pdb=" OE1 GLN B 230 " model vdw 2.243 2.520 ... (remaining 136205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 106 through 620 or resid 801)) selection = (chain 'B' and (resid 106 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 198 through 620 or resid 801)) selection = (chain 'C' and (resid 106 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 198 through 620 or resid 801)) selection = (chain 'D' and (resid 106 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 198 through 620 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 2.850 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 43.140 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.015 0.309 17375 Z= 0.909 Angle : 1.484 11.805 23586 Z= 0.966 Chirality : 0.082 1.307 2612 Planarity : 0.006 0.051 2904 Dihedral : 16.005 88.644 6351 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.98 % Favored : 93.43 % Rotamer Outliers : 6.55 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 13.33 % 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: -3.19 (0.16), residues: 2024 helix: -2.41 (0.12), residues: 1072 sheet: -0.98 (0.47), residues: 120 loop : -1.63 (0.21), residues: 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 545 time to evaluate : 2.079 Fit side-chains outliers start: 121 outliers final: 37 residues processed: 637 average time/residue: 0.3133 time to fit residues: 287.2926 Evaluate side-chains 406 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 369 time to evaluate : 2.041 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1570 time to fit residues: 13.6867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9990 chunk 154 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.0020 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.4980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 323 ASN A 416 ASN A 426 ASN B 143 GLN B 323 ASN B 416 ASN B 426 ASN C 143 GLN C 272 ASN C 323 ASN C 416 ASN C 426 ASN D 143 GLN D 175 ASN D 323 ASN D 416 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 17375 Z= 0.165 Angle : 0.627 7.697 23586 Z= 0.317 Chirality : 0.043 0.144 2612 Planarity : 0.004 0.029 2904 Dihedral : 4.779 21.847 2295 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.15 (0.19), residues: 2024 helix: 0.53 (0.16), residues: 1088 sheet: -0.72 (0.47), residues: 120 loop : -0.74 (0.22), residues: 816 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 470 time to evaluate : 2.180 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 13 residues processed: 488 average time/residue: 0.2889 time to fit residues: 210.2045 Evaluate side-chains 370 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 357 time to evaluate : 1.913 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1457 time to fit residues: 6.2348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 154 optimal weight: 0.0970 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 200 optimal weight: 0.0970 chunk 165 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 169 GLN A 347 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN B 143 GLN B 175 ASN B 416 ASN C 143 GLN C 175 ASN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN D 143 GLN D 416 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 17375 Z= 0.308 Angle : 0.674 10.078 23586 Z= 0.337 Chirality : 0.044 0.158 2612 Planarity : 0.004 0.044 2904 Dihedral : 4.871 24.474 2295 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.31 (0.18), residues: 2024 helix: 0.95 (0.15), residues: 1044 sheet: -0.67 (0.47), residues: 120 loop : -0.49 (0.21), residues: 860 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 370 time to evaluate : 2.240 Fit side-chains outliers start: 81 outliers final: 40 residues processed: 415 average time/residue: 0.2499 time to fit residues: 163.0317 Evaluate side-chains 370 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 330 time to evaluate : 1.950 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.1477 time to fit residues: 13.8230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 272 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 272 ASN C 143 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN D 175 ASN D 272 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 17375 Z= 0.287 Angle : 0.635 8.880 23586 Z= 0.320 Chirality : 0.044 0.154 2612 Planarity : 0.004 0.046 2904 Dihedral : 4.824 23.619 2295 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2024 helix: 1.07 (0.15), residues: 1044 sheet: -0.73 (0.52), residues: 116 loop : -0.52 (0.21), residues: 864 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 353 time to evaluate : 2.199 Fit side-chains outliers start: 52 outliers final: 24 residues processed: 392 average time/residue: 0.2621 time to fit residues: 161.9534 Evaluate side-chains 355 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 331 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1562 time to fit residues: 9.9091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 169 GLN C 143 GLN C 169 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN D 169 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 17375 Z= 0.228 Angle : 0.600 8.451 23586 Z= 0.299 Chirality : 0.042 0.145 2612 Planarity : 0.004 0.045 2904 Dihedral : 4.650 23.044 2295 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 2024 helix: 1.25 (0.16), residues: 1032 sheet: -0.84 (0.51), residues: 116 loop : -0.32 (0.21), residues: 876 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 367 time to evaluate : 2.090 Fit side-chains outliers start: 45 outliers final: 24 residues processed: 398 average time/residue: 0.2851 time to fit residues: 172.8431 Evaluate side-chains 361 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 337 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1643 time to fit residues: 10.3038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN C 143 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 17375 Z= 0.229 Angle : 0.597 9.485 23586 Z= 0.297 Chirality : 0.041 0.139 2612 Planarity : 0.004 0.044 2904 Dihedral : 4.555 22.477 2295 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.72 (0.19), residues: 2024 helix: 1.27 (0.16), residues: 1040 sheet: -0.83 (0.52), residues: 116 loop : -0.22 (0.22), residues: 868 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 343 time to evaluate : 2.434 Fit side-chains outliers start: 44 outliers final: 25 residues processed: 364 average time/residue: 0.2619 time to fit residues: 148.5777 Evaluate side-chains 356 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 331 time to evaluate : 2.247 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1611 time to fit residues: 10.4766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 196 optimal weight: 0.4980 chunk 123 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 17375 Z= 0.215 Angle : 0.599 10.005 23586 Z= 0.297 Chirality : 0.042 0.148 2612 Planarity : 0.004 0.044 2904 Dihedral : 4.493 21.959 2295 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.79 (0.19), residues: 2024 helix: 1.34 (0.16), residues: 1036 sheet: -0.89 (0.53), residues: 116 loop : -0.16 (0.22), residues: 872 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 343 time to evaluate : 2.202 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 354 average time/residue: 0.2510 time to fit residues: 138.8522 Evaluate side-chains 336 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 327 time to evaluate : 1.930 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1652 time to fit residues: 5.3259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.0470 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 17375 Z= 0.142 Angle : 0.578 11.082 23586 Z= 0.280 Chirality : 0.040 0.137 2612 Planarity : 0.004 0.044 2904 Dihedral : 4.154 19.511 2295 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.03 (0.19), residues: 2024 helix: 1.53 (0.16), residues: 1060 sheet: -0.79 (0.53), residues: 116 loop : -0.08 (0.22), residues: 848 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 384 time to evaluate : 2.111 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 394 average time/residue: 0.2699 time to fit residues: 165.9108 Evaluate side-chains 367 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 357 time to evaluate : 2.079 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1623 time to fit residues: 5.8369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 165 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 17375 Z= 0.227 Angle : 0.647 11.016 23586 Z= 0.313 Chirality : 0.043 0.179 2612 Planarity : 0.004 0.050 2904 Dihedral : 4.427 20.115 2295 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.19), residues: 2024 helix: 1.40 (0.16), residues: 1036 sheet: -0.69 (0.54), residues: 116 loop : -0.19 (0.21), residues: 872 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 344 time to evaluate : 2.183 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 354 average time/residue: 0.2654 time to fit residues: 147.6694 Evaluate side-chains 340 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 329 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1657 time to fit residues: 6.2193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 8.9990 chunk 118 optimal weight: 0.0970 chunk 91 optimal weight: 4.9990 chunk 134 optimal weight: 0.1980 chunk 203 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 17375 Z= 0.147 Angle : 0.624 12.146 23586 Z= 0.297 Chirality : 0.041 0.165 2612 Planarity : 0.004 0.046 2904 Dihedral : 4.129 18.266 2295 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 2024 helix: 1.50 (0.16), residues: 1060 sheet: -0.59 (0.54), residues: 116 loop : -0.11 (0.21), residues: 848 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 369 time to evaluate : 2.158 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 372 average time/residue: 0.2560 time to fit residues: 149.9122 Evaluate side-chains 353 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 348 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1810 time to fit residues: 4.3934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 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 = 0.3914 r_free = 0.3914 target = 0.161574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119207 restraints weight = 25339.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122103 restraints weight = 13374.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123501 restraints weight = 9420.533| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 17375 Z= 0.211 Angle : 0.668 13.353 23586 Z= 0.317 Chirality : 0.043 0.180 2612 Planarity : 0.004 0.050 2904 Dihedral : 4.293 19.094 2295 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.89 (0.19), residues: 2024 helix: 1.38 (0.16), residues: 1060 sheet: -0.53 (0.56), residues: 116 loop : -0.15 (0.21), residues: 848 =============================================================================== Job complete usr+sys time: 3584.23 seconds wall clock time: 65 minutes 49.48 seconds (3949.48 seconds total)