Starting phenix.real_space_refine on Fri Nov 17 01:06:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apd_11852/11_2023/7apd_11852.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apd_11852/11_2023/7apd_11852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apd_11852/11_2023/7apd_11852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apd_11852/11_2023/7apd_11852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apd_11852/11_2023/7apd_11852.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7apd_11852/11_2023/7apd_11852.pdb" } resolution = 3.9 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= 0.048 sd= 0.782 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 76 5.49 5 S 78 5.16 5 C 10876 2.51 5 N 3005 2.21 5 O 3261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 294": "OE1" <-> "OE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B ASP 479": "OD1" <-> "OD2" Residue "B ASP 489": "OD1" <-> "OD2" Residue "B ASP 497": "OD1" <-> "OD2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B ASP 525": "OD1" <-> "OD2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B ASP 530": "OD1" <-> "OD2" Residue "B ASP 561": "OD1" <-> "OD2" Residue "B PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 479": "OD1" <-> "OD2" Residue "C TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C ASP 530": "OD1" <-> "OD2" Residue "C TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 563": "OD1" <-> "OD2" Residue "C PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "D TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 327": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 489": "OD1" <-> "OD2" Residue "D ASP 525": "OD1" <-> "OD2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E ASP 342": "OD1" <-> "OD2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 392": "OE1" <-> "OE2" Residue "E PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 479": "OD1" <-> "OD2" Residue "E ASP 504": "OD1" <-> "OD2" Residue "E ASP 525": "OD1" <-> "OD2" Residue "E ASP 530": "OD1" <-> "OD2" Residue "E TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 545": "OE1" <-> "OE2" Residue "F PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 392": "OE1" <-> "OE2" Residue "F PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 504": "OD1" <-> "OD2" Residue "F ASP 525": "OD1" <-> "OD2" Residue "F ASP 530": "OD1" <-> "OD2" Residue "F TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 545": "OE1" <-> "OE2" Residue "F ASP 561": "OD1" <-> "OD2" Residue "F ASP 563": "OD1" <-> "OD2" Residue "F PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 576": "OD1" <-> "OD2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 563": "OD1" <-> "OD2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 17296 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1201 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 146} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2238 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 279} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2228 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2228 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2232 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2229 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 276} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2213 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 51 Chain: "H" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1184 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "P" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 805 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N GLY H 156 " occ=0.60 ... (2 atoms not shown) pdb=" O GLY H 156 " occ=0.60 residue: pdb=" N SER H 157 " occ=0.60 ... (4 atoms not shown) pdb=" OG SER H 157 " occ=0.60 residue: pdb=" N ARG H 158 " occ=0.60 ... (9 atoms not shown) pdb=" NH2 ARG H 158 " occ=0.60 Time building chain proxies: 9.45, per 1000 atoms: 0.55 Number of scatterers: 17296 At special positions: 0 Unit cell: (135.625, 157.325, 116.095, 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 78 16.00 P 76 15.00 O 3261 8.00 N 3005 7.00 C 10876 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: 7.56 Conformation dependent library (CDL) restraints added in 2.9 seconds 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 13 sheets defined 53.3% alpha, 8.2% beta 15 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 6.07 Creating SS restraints... Processing helix chain 'G' and resid 160 through 172 Processing helix chain 'G' and resid 200 through 212 Processing helix chain 'G' and resid 242 through 254 Processing helix chain 'G' and resid 271 through 281 removed outlier: 4.818A pdb=" N TRP G 277 " --> pdb=" O ALA G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 342 through 351 removed outlier: 3.518A pdb=" N THR B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 376 removed outlier: 4.211A pdb=" N LEU B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 388 Processing helix chain 'B' and resid 395 through 405 Processing helix chain 'B' and resid 408 through 421 removed outlier: 4.056A pdb=" N PHE B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 451 removed outlier: 3.797A pdb=" N LEU B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 removed outlier: 4.046A pdb=" N HIS B 463 " --> pdb=" O HIS B 460 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 464 " --> pdb=" O LYS B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 464' Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 481 through 491 Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.676A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 532 through 537 removed outlier: 4.622A pdb=" N SER B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 571 Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.158A pdb=" N PHE B 594 " --> pdb=" O MET B 591 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 595 " --> pdb=" O ARG B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 595' Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 327 through 339 Processing helix chain 'C' and resid 342 through 350 removed outlier: 3.776A pdb=" N ALA C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 374 Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'C' and resid 408 through 420 removed outlier: 3.927A pdb=" N PHE C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.774A pdb=" N ASN C 459 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS C 461 " --> pdb=" O ALA C 458 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS C 463 " --> pdb=" O HIS C 460 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE C 464 " --> pdb=" O LYS C 461 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 466 " --> pdb=" O HIS C 463 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER C 468 " --> pdb=" O TRP C 465 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 470 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 491 Processing helix chain 'C' and resid 492 through 498 Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'C' and resid 560 through 571 removed outlier: 3.990A pdb=" N TRP C 564 " --> pdb=" O THR C 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.639A pdb=" N MET D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 Processing helix chain 'D' and resid 342 through 350 removed outlier: 4.080A pdb=" N ALA D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 376 Processing helix chain 'D' and resid 377 through 387 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.570A pdb=" N LEU D 399 " --> pdb=" O TRP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 422 removed outlier: 3.981A pdb=" N PHE D 412 " --> pdb=" O GLU D 408 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU D 418 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 450 Processing helix chain 'D' and resid 456 through 460 removed outlier: 4.053A pdb=" N ASN D 459 " --> pdb=" O SER D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 471 removed outlier: 4.120A pdb=" N LEU D 466 " --> pdb=" O HIS D 463 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER D 468 " --> pdb=" O TRP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 491 Processing helix chain 'D' and resid 492 through 498 Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.551A pdb=" N LEU D 533 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 571 Processing helix chain 'E' and resid 312 through 324 removed outlier: 3.592A pdb=" N MET E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 339 Processing helix chain 'E' and resid 342 through 349 Processing helix chain 'E' and resid 353 through 374 Processing helix chain 'E' and resid 377 through 389 Processing helix chain 'E' and resid 395 through 406 removed outlier: 4.815A pdb=" N PHE E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 422 removed outlier: 3.991A pdb=" N PHE E 412 " --> pdb=" O GLU E 408 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU E 418 " --> pdb=" O ASN E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 450 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.675A pdb=" N ASN E 459 " --> pdb=" O SER E 456 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS E 461 " --> pdb=" O ALA E 458 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS E 463 " --> pdb=" O HIS E 460 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE E 464 " --> pdb=" O LYS E 461 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU E 466 " --> pdb=" O HIS E 463 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E 468 " --> pdb=" O TRP E 465 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP E 471 " --> pdb=" O SER E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 491 Processing helix chain 'E' and resid 492 through 498 removed outlier: 3.684A pdb=" N LEU E 496 " --> pdb=" O LEU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 removed outlier: 3.582A pdb=" N HIS E 536 " --> pdb=" O LEU E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 571 removed outlier: 4.049A pdb=" N TRP E 564 " --> pdb=" O THR E 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 324 removed outlier: 3.522A pdb=" N MET F 316 " --> pdb=" O ASP F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 339 Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 353 through 375 Processing helix chain 'F' and resid 377 through 389 removed outlier: 3.715A pdb=" N LEU F 388 " --> pdb=" O ALA F 384 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 405 Processing helix chain 'F' and resid 408 through 422 removed outlier: 3.804A pdb=" N PHE F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU F 418 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS F 421 " --> pdb=" O LYS F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 450 Processing helix chain 'F' and resid 456 through 462 removed outlier: 3.601A pdb=" N ASN F 459 " --> pdb=" O SER F 456 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS F 461 " --> pdb=" O ALA F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'F' and resid 481 through 492 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 532 through 538 removed outlier: 3.556A pdb=" N HIS F 536 " --> pdb=" O LEU F 533 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER F 537 " --> pdb=" O TYR F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 571 removed outlier: 3.595A pdb=" N TRP F 564 " --> pdb=" O THR F 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.645A pdb=" N ALA A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.671A pdb=" N PHE A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 456 through 460 removed outlier: 3.757A pdb=" N ASN A 459 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 removed outlier: 3.749A pdb=" N ALA A 470 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 491 Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.506A pdb=" N LEU A 496 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 576 removed outlier: 6.019A pdb=" N GLY A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ARG A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 172 Processing helix chain 'H' and resid 174 through 178 Processing helix chain 'H' and resid 200 through 213 removed outlier: 3.744A pdb=" N GLU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 255 Processing helix chain 'H' and resid 257 through 259 No H-bonds generated for 'chain 'H' and resid 257 through 259' Processing helix chain 'H' and resid 270 through 281 removed outlier: 3.858A pdb=" N TRP H 277 " --> pdb=" O ALA H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 298 Processing sheet with id=AA1, first strand: chain 'G' and resid 189 through 197 removed outlier: 6.180A pdb=" N GLN G 190 " --> pdb=" O PHE G 237 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE G 217 " --> pdb=" O CYS G 236 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASN G 238 " --> pdb=" O CYS G 215 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N CYS G 215 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 518 through 522 removed outlier: 3.947A pdb=" N LEU B 429 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 522 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N CYS B 428 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE B 542 " --> pdb=" O CYS B 428 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA B 430 " --> pdb=" O PHE B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 501 through 504 Processing sheet with id=AA4, first strand: chain 'C' and resid 453 through 455 removed outlier: 4.619A pdb=" N ASP C 478 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA C 475 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR C 521 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL C 477 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 522 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 430 " --> pdb=" O PHE C 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 501 through 503 removed outlier: 3.578A pdb=" N VAL C 501 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 513 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 454 through 455 removed outlier: 4.347A pdb=" N ASP D 478 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D 521 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 429 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS D 428 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE D 542 " --> pdb=" O CYS D 428 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA D 430 " --> pdb=" O PHE D 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 501 through 503 Processing sheet with id=AA8, first strand: chain 'E' and resid 475 through 478 removed outlier: 6.075A pdb=" N LEU E 429 " --> pdb=" O VAL E 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 501 through 503 removed outlier: 3.791A pdb=" N ILE E 503 " --> pdb=" O VAL E 511 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 453 through 454 removed outlier: 7.127A pdb=" N SER F 453 " --> pdb=" O LEU F 476 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASP F 478 " --> pdb=" O SER F 453 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU F 519 " --> pdb=" O LEU F 476 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP F 478 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR F 521 " --> pdb=" O ASP F 478 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU F 429 " --> pdb=" O VAL F 520 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N SER F 522 " --> pdb=" O LEU F 429 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N PHE F 431 " --> pdb=" O SER F 522 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 501 through 503 Processing sheet with id=AB3, first strand: chain 'A' and resid 477 through 480 removed outlier: 6.332A pdb=" N ASP A 478 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR A 521 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A 429 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER A 522 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE A 431 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS A 428 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE A 542 " --> pdb=" O CYS A 428 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 430 " --> pdb=" O PHE A 542 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 261 through 264 removed outlier: 5.558A pdb=" N GLN H 190 " --> pdb=" O PHE H 237 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N CYS H 230 " --> pdb=" O LYS H 222 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS H 222 " --> pdb=" O CYS H 230 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL H 232 " --> pdb=" O MET H 220 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET H 220 " --> pdb=" O VAL H 232 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU H 234 " --> pdb=" O LEU H 218 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU H 218 " --> pdb=" O LEU H 234 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N CYS H 236 " --> pdb=" O SER H 216 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 1983 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 8.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5288 1.34 - 1.48: 5126 1.48 - 1.61: 7330 1.61 - 1.74: 26 1.74 - 1.87: 110 Bond restraints: 17880 Sorted by residual: bond pdb=" C1' DG T 68 " pdb=" N9 DG T 68 " ideal model delta sigma weight residual 1.460 1.373 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C1' DG T 63 " pdb=" N9 DG T 63 " ideal model delta sigma weight residual 1.460 1.377 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1' DG T 49 " pdb=" N9 DG T 49 " ideal model delta sigma weight residual 1.460 1.383 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C1' DG T 70 " pdb=" N9 DG T 70 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1' DG T 58 " pdb=" N9 DG T 58 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 17875 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.10: 394 104.10 - 111.60: 8300 111.60 - 119.10: 6096 119.10 - 126.60: 9309 126.60 - 134.10: 468 Bond angle restraints: 24567 Sorted by residual: angle pdb=" CA ARG G 297 " pdb=" CB ARG G 297 " pdb=" CG ARG G 297 " ideal model delta sigma weight residual 114.10 131.61 -17.51 2.00e+00 2.50e-01 7.66e+01 angle pdb=" N LYS B 506 " pdb=" CA LYS B 506 " pdb=" C LYS B 506 " ideal model delta sigma weight residual 113.19 123.13 -9.94 1.19e+00 7.06e-01 6.98e+01 angle pdb=" C LEU G 302 " pdb=" N ASN G 303 " pdb=" CA ASN G 303 " ideal model delta sigma weight residual 122.87 109.86 13.01 1.61e+00 3.86e-01 6.53e+01 angle pdb=" N LEU H 181 " pdb=" CA LEU H 181 " pdb=" C LEU H 181 " ideal model delta sigma weight residual 109.24 121.79 -12.55 1.63e+00 3.76e-01 5.93e+01 angle pdb=" N LEU H 234 " pdb=" CA LEU H 234 " pdb=" C LEU H 234 " ideal model delta sigma weight residual 108.52 98.56 9.96 1.63e+00 3.76e-01 3.74e+01 ... (remaining 24562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 9369 28.35 - 56.69: 749 56.69 - 85.04: 125 85.04 - 113.38: 9 113.38 - 141.73: 1 Dihedral angle restraints: 10253 sinusoidal: 4311 harmonic: 5942 Sorted by residual: dihedral pdb=" CA ARG G 180 " pdb=" C ARG G 180 " pdb=" N LEU G 181 " pdb=" CA LEU G 181 " ideal model delta harmonic sigma weight residual 180.00 -143.51 -36.49 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA LYS G 213 " pdb=" C LYS G 213 " pdb=" N GLN G 214 " pdb=" CA GLN G 214 " ideal model delta harmonic sigma weight residual -180.00 -146.84 -33.16 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA ARG G 223 " pdb=" C ARG G 223 " pdb=" N SER G 224 " pdb=" CA SER G 224 " ideal model delta harmonic sigma weight residual 0.00 26.01 -26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 10250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2426 0.078 - 0.156: 235 0.156 - 0.234: 30 0.234 - 0.312: 8 0.312 - 0.390: 8 Chirality restraints: 2707 Sorted by residual: chirality pdb=" CA LYS B 506 " pdb=" N LYS B 506 " pdb=" C LYS B 506 " pdb=" CB LYS B 506 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA PHE H 182 " pdb=" N PHE H 182 " pdb=" C PHE H 182 " pdb=" CB PHE H 182 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE D 559 " pdb=" CA ILE D 559 " pdb=" CG1 ILE D 559 " pdb=" CG2 ILE D 559 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 2704 not shown) Planarity restraints: 2855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 334 " -0.026 2.00e-02 2.50e+03 5.26e-02 2.77e+01 pdb=" CD GLU A 334 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLU A 334 " -0.033 2.00e-02 2.50e+03 pdb=" OE2 GLU A 334 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 197 " -0.056 2.00e-02 2.50e+03 3.42e-02 2.05e+01 pdb=" CG PHE H 197 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE H 197 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE H 197 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE H 197 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE H 197 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 197 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 192 " -0.060 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP H 192 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 192 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP H 192 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 192 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 192 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 192 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 192 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 192 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 192 " -0.022 2.00e-02 2.50e+03 ... (remaining 2852 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 15 2.06 - 2.77: 3350 2.77 - 3.48: 23641 3.48 - 4.19: 38511 4.19 - 4.90: 67504 Nonbonded interactions: 133021 Sorted by model distance: nonbonded pdb=" O MET E 591 " pdb=" O6 DG T 49 " model vdw 1.349 3.040 nonbonded pdb=" N1 DA P 9 " pdb=" O6 DG T 70 " model vdw 1.357 2.496 nonbonded pdb=" OG1 THR G 187 " pdb=" C7 DT T 69 " model vdw 1.575 3.460 nonbonded pdb=" O LEU H 172 " pdb=" C5' DC T 46 " model vdw 1.679 3.440 nonbonded pdb=" O6 DG P 24 " pdb=" O6 DG T 55 " model vdw 1.783 3.040 ... (remaining 133016 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' and resid 308 through 591) selection = (chain 'C' and resid 308 through 591) selection = (chain 'D' and resid 308 through 591) selection = (chain 'E' and ((resid 308 through 309 and (name N or name CA or name C or name \ O or name CB )) or resid 310 through 591)) selection = (chain 'F' and ((resid 308 through 309 and (name N or name CA or name C or name \ O or name CB )) or resid 310 through 591)) } ncs_group { reference = (chain 'G' and resid 156 through 303) selection = (chain 'H' and (resid 156 through 302 or (resid 303 and (name N or name CA or na \ me C or name O or name CB )))) } 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=0.00 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: 2.490 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: 6.600 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 51.080 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.080 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 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 : 0.006 0.087 17880 Z= 0.375 Angle : 0.839 17.506 24567 Z= 0.492 Chirality : 0.054 0.390 2707 Planarity : 0.004 0.088 2855 Dihedral : 19.769 141.730 6397 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.48 % Favored : 91.37 % Rotamer: Outliers : 2.92 % Allowed : 1.33 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.18), residues: 2004 helix: -0.55 (0.16), residues: 972 sheet: -1.67 (0.36), residues: 206 loop : -2.06 (0.20), residues: 826 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 220 time to evaluate : 1.941 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 6 residues processed: 256 average time/residue: 0.3246 time to fit residues: 121.0681 Evaluate side-chains 168 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2903 time to fit residues: 4.9843 ------------------------------------------------------------------------------- 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: 1.9990 chunk 154 optimal weight: 10.0000 chunk 85 optimal weight: 0.0770 chunk 52 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 221 GLN G 264 GLN ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 444 ASN ** D 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS E 367 HIS ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 ASN A 344 ASN A 406 ASN A 444 ASN H 176 HIS H 225 HIS H 248 ASN H 264 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17880 Z= 0.224 Angle : 0.627 9.031 24567 Z= 0.341 Chirality : 0.041 0.255 2707 Planarity : 0.004 0.064 2855 Dihedral : 19.515 142.024 2934 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 1.65 % Allowed : 9.85 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 2004 helix: -0.05 (0.16), residues: 987 sheet: -1.48 (0.36), residues: 201 loop : -1.63 (0.22), residues: 816 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 1.856 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 201 average time/residue: 0.3110 time to fit residues: 94.7693 Evaluate side-chains 181 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.947 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1708 time to fit residues: 8.0378 ------------------------------------------------------------------------------- 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: 0.6980 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 189 ASN G 219 GLN G 221 GLN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN C 374 GLN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS D 436 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17880 Z= 0.215 Angle : 0.563 8.951 24567 Z= 0.308 Chirality : 0.039 0.193 2707 Planarity : 0.003 0.053 2855 Dihedral : 19.370 141.336 2934 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.46 % Allowed : 12.90 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 2004 helix: 0.17 (0.16), residues: 981 sheet: -1.33 (0.37), residues: 192 loop : -1.43 (0.22), residues: 831 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 2.056 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 187 average time/residue: 0.3018 time to fit residues: 86.1120 Evaluate side-chains 173 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1668 time to fit residues: 5.9276 ------------------------------------------------------------------------------- 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: 9.9990 chunk 139 optimal weight: 0.0040 chunk 96 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN C 512 GLN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN A 444 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17880 Z= 0.170 Angle : 0.528 9.380 24567 Z= 0.288 Chirality : 0.038 0.147 2707 Planarity : 0.003 0.046 2855 Dihedral : 19.187 141.582 2934 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.52 % Allowed : 14.36 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.75 (0.19), residues: 2004 helix: 0.37 (0.16), residues: 979 sheet: -1.13 (0.38), residues: 185 loop : -1.32 (0.22), residues: 840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.816 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 204 average time/residue: 0.3094 time to fit residues: 94.5184 Evaluate side-chains 172 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1641 time to fit residues: 5.8661 ------------------------------------------------------------------------------- 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: 0.8980 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN D 436 ASN D 444 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 HIS F 482 HIS A 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17880 Z= 0.225 Angle : 0.557 9.069 24567 Z= 0.302 Chirality : 0.039 0.219 2707 Planarity : 0.003 0.045 2855 Dihedral : 19.110 139.671 2934 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.08 % Allowed : 16.07 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.76 (0.19), residues: 2004 helix: 0.39 (0.16), residues: 984 sheet: -1.10 (0.35), residues: 210 loop : -1.37 (0.22), residues: 810 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 1.943 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 181 average time/residue: 0.3111 time to fit residues: 85.6723 Evaluate side-chains 167 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 157 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1781 time to fit residues: 6.4234 ------------------------------------------------------------------------------- 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: 1.9990 chunk 177 optimal weight: 0.0970 chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 163 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17880 Z= 0.236 Angle : 0.555 9.672 24567 Z= 0.302 Chirality : 0.039 0.230 2707 Planarity : 0.003 0.047 2855 Dihedral : 19.095 139.314 2934 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.46 % Allowed : 16.96 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.76 (0.19), residues: 2004 helix: 0.42 (0.16), residues: 979 sheet: -1.14 (0.34), residues: 211 loop : -1.42 (0.22), residues: 814 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.990 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 174 average time/residue: 0.3164 time to fit residues: 83.8968 Evaluate side-chains 160 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2092 time to fit residues: 6.9097 ------------------------------------------------------------------------------- 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: 0.0570 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 196 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 0.0870 chunk 90 optimal weight: 0.9980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 GLN E 323 HIS ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17880 Z= 0.160 Angle : 0.525 12.445 24567 Z= 0.280 Chirality : 0.037 0.221 2707 Planarity : 0.003 0.043 2855 Dihedral : 18.930 141.230 2934 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.57 % Allowed : 17.60 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.48 (0.19), residues: 2004 helix: 0.62 (0.17), residues: 982 sheet: -1.04 (0.35), residues: 209 loop : -1.22 (0.22), residues: 813 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 168 time to evaluate : 1.866 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 174 average time/residue: 0.3453 time to fit residues: 90.7242 Evaluate side-chains 157 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 2.359 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3023 time to fit residues: 5.5291 ------------------------------------------------------------------------------- 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: 0.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 178 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17880 Z= 0.184 Angle : 0.536 10.778 24567 Z= 0.285 Chirality : 0.038 0.225 2707 Planarity : 0.003 0.046 2855 Dihedral : 18.887 139.941 2934 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.44 % Allowed : 18.30 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.44 (0.19), residues: 2004 helix: 0.65 (0.17), residues: 980 sheet: -0.98 (0.35), residues: 209 loop : -1.21 (0.22), residues: 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 1.904 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 164 average time/residue: 0.3021 time to fit residues: 76.0122 Evaluate side-chains 155 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1667 time to fit residues: 3.4457 ------------------------------------------------------------------------------- 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: 0.3980 chunk 171 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 165 optimal weight: 0.8980 chunk 173 optimal weight: 0.5980 chunk 182 optimal weight: 0.4980 chunk 120 optimal weight: 0.2980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17880 Z= 0.145 Angle : 0.506 9.447 24567 Z= 0.270 Chirality : 0.036 0.204 2707 Planarity : 0.003 0.045 2855 Dihedral : 18.694 140.982 2934 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.38 % Allowed : 18.74 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.26 (0.19), residues: 2004 helix: 0.78 (0.17), residues: 982 sheet: -0.82 (0.36), residues: 209 loop : -1.12 (0.22), residues: 813 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 2.022 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 176 average time/residue: 0.3138 time to fit residues: 83.4569 Evaluate side-chains 159 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1624 time to fit residues: 2.8958 ------------------------------------------------------------------------------- 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: 9.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 187 optimal weight: 0.0980 chunk 161 optimal weight: 0.0770 chunk 16 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17880 Z= 0.160 Angle : 0.515 9.904 24567 Z= 0.275 Chirality : 0.037 0.220 2707 Planarity : 0.003 0.035 2855 Dihedral : 18.636 139.718 2934 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.38 % Allowed : 18.81 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.20 (0.19), residues: 2004 helix: 0.83 (0.17), residues: 982 sheet: -0.71 (0.37), residues: 204 loop : -1.12 (0.22), residues: 818 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 1.827 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 158 average time/residue: 0.3072 time to fit residues: 73.7944 Evaluate side-chains 155 residues out of total 1714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 2.020 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1545 time to fit residues: 4.0718 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 166 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.165150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144670 restraints weight = 25640.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144049 restraints weight = 30489.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144081 restraints weight = 27758.391| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17880 Z= 0.172 Angle : 0.520 9.772 24567 Z= 0.278 Chirality : 0.037 0.224 2707 Planarity : 0.003 0.051 2855 Dihedral : 18.623 139.542 2934 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.13 % Allowed : 19.25 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.20 (0.19), residues: 2004 helix: 0.82 (0.17), residues: 982 sheet: -0.69 (0.37), residues: 204 loop : -1.12 (0.22), residues: 818 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3043.57 seconds wall clock time: 56 minutes 33.70 seconds (3393.70 seconds total)