Starting phenix.real_space_refine on Sat Mar 16 23:03:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/03_2024/7l8y_23240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/03_2024/7l8y_23240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/03_2024/7l8y_23240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/03_2024/7l8y_23240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/03_2024/7l8y_23240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/03_2024/7l8y_23240_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 9901 2.51 5 N 2711 2.21 5 O 3186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 585": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15903 Number of models: 1 Model: "" Number of chains: 27 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3447 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 20, 'TRANS': 416} Chain breaks: 3 Chain: "D" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1131 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "A" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3460 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "E" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3434 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.77, per 1000 atoms: 0.55 Number of scatterers: 15903 At special positions: 0 Unit cell: (133.9, 161.71, 123.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3186 8.00 N 2711 7.00 C 9901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.01 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 295 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 160 " " NAG A 610 " - " ASN A 197 " " NAG A 611 " - " ASN A 133 " " NAG A 612 " - " ASN A 355 " " NAG A 613 " - " ASN A 289 " " NAG A 614 " - " ASN A 462 " " NAG A 615 " - " ASN A 339 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 332 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 448 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 197 " " NAG C 609 " - " ASN C 133 " " NAG C 610 " - " ASN C 289 " " NAG C 611 " - " ASN C 137 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 448 " " NAG E 609 " - " ASN E 301 " " NAG E 610 " - " ASN E 160 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 133 " " NAG E 613 " - " ASN E 355 " " NAG E 614 " - " ASN E 289 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN C 392 " " NAG I 1 " - " ASN C 386 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 156 " " NAG M 1 " - " ASN C 160 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN E 386 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 262 " " NAG U 1 " - " ASN E 156 " Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 36 sheets defined 29.7% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'L' and resid 28 through 30 No H-bonds generated for 'chain 'L' and resid 28 through 30' Processing helix chain 'L' and resid 60 through 62 No H-bonds generated for 'chain 'L' and resid 60 through 62' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 352 removed outlier: 4.219A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 475 through 485 removed outlier: 3.776A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 565 removed outlier: 4.402A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 557 " --> pdb=" O SER D 553 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA D 558 " --> pdb=" O ASN D 554 " (cutoff:3.500A) Proline residue: D 559 - end of helix removed outlier: 4.036A pdb=" N GLN D 562 " --> pdb=" O ALA D 558 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN D 563 " --> pdb=" O PRO D 559 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N HIS D 564 " --> pdb=" O GLU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 595 Processing helix chain 'D' and resid 621 through 624 No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 661 removed outlier: 4.109A pdb=" N THR D 639 " --> pdb=" O SER D 636 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR D 643 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 654 " --> pdb=" O ASN D 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.563A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.935A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 485 removed outlier: 4.396A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 567 removed outlier: 5.219A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 540 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 542 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 544 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 546 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY B 547 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 556 " --> pdb=" O SER B 553 " (cutoff:3.500A) Proline residue: B 559 - end of helix removed outlier: 4.387A pdb=" N GLN B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 566 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 620 through 623 No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 661 removed outlier: 5.153A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 654 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 352 removed outlier: 4.237A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 475 through 485 removed outlier: 4.538A pdb=" N SER E 481 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 567 removed outlier: 4.813A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA F 558 " --> pdb=" O ASN F 554 " (cutoff:3.500A) Proline residue: F 559 - end of helix removed outlier: 5.095A pdb=" N HIS F 564 " --> pdb=" O GLU F 560 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU F 565 " --> pdb=" O CYS F 561 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU F 566 " --> pdb=" O GLN F 562 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS F 567 " --> pdb=" O GLN F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 612 through 615 No H-bonds generated for 'chain 'F' and resid 612 through 615' Processing helix chain 'F' and resid 619 through 621 No H-bonds generated for 'chain 'F' and resid 619 through 621' Processing helix chain 'F' and resid 628 through 662 removed outlier: 4.511A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'H' and resid 33 through 36 Processing sheet with id= C, first strand: chain 'H' and resid 91 through 94 Processing sheet with id= D, first strand: chain 'L' and resid 6 through 8 Processing sheet with id= E, first strand: chain 'L' and resid 36 through 39 removed outlier: 3.644A pdb=" N UNK L 85 " --> pdb=" O UNK L 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= G, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.715A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= J, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= K, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= L, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= M, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.251A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.001A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.454A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= Q, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= R, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= S, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= T, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= U, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= V, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.555A pdb=" N ALA A 433 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.417A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.094A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.419A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= AA, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= AB, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= AC, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= AD, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= AE, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AF, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= AG, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.451A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 414 through 417 removed outlier: 6.542A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.312A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3687 1.32 - 1.46: 5040 1.46 - 1.60: 7295 1.60 - 1.74: 18 1.74 - 1.88: 134 Bond restraints: 16174 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.393 0.104 1.40e-02 5.10e+03 5.54e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.395 -0.069 1.10e-02 8.26e+03 3.98e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.84e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.72e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.650 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 16169 not shown) Histogram of bond angle deviations from ideal: 96.36 - 104.01: 182 104.01 - 111.66: 7613 111.66 - 119.32: 6516 119.32 - 126.97: 7455 126.97 - 134.62: 235 Bond angle restraints: 22001 Sorted by residual: angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 128.44 -8.88 1.02e+00 9.61e-01 7.58e+01 angle pdb=" C LEU F 523 " pdb=" N GLY F 524 " pdb=" CA GLY F 524 " ideal model delta sigma weight residual 120.10 128.29 -8.19 9.50e-01 1.11e+00 7.42e+01 angle pdb=" N ILE F 622 " pdb=" CA ILE F 622 " pdb=" C ILE F 622 " ideal model delta sigma weight residual 111.67 103.60 8.07 9.50e-01 1.11e+00 7.21e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.34 -7.78 1.01e+00 9.80e-01 5.93e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.32 -7.76 1.01e+00 9.80e-01 5.90e+01 ... (remaining 21996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 10484 21.29 - 42.58: 194 42.58 - 63.88: 73 63.88 - 85.17: 32 85.17 - 106.46: 13 Dihedral angle restraints: 10796 sinusoidal: 5140 harmonic: 5656 Sorted by residual: dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.02 -66.02 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.31 -60.31 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.22 -60.22 1 1.00e+01 1.00e-02 4.83e+01 ... (remaining 10793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 2317 0.169 - 0.338: 353 0.338 - 0.507: 102 0.507 - 0.676: 1 0.676 - 0.845: 1 Chirality restraints: 2774 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 2771 not shown) Planarity restraints: 2776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 610 " -0.349 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG C 610 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C 610 " -0.128 2.00e-02 2.50e+03 pdb=" N2 NAG C 610 " 0.535 2.00e-02 2.50e+03 pdb=" O7 NAG C 610 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 606 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG E 606 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG E 606 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG E 606 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG E 606 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B 702 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.074 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " 0.185 2.00e-02 2.50e+03 ... (remaining 2773 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1762 2.73 - 3.27: 15212 3.27 - 3.82: 24698 3.82 - 4.36: 31835 4.36 - 4.90: 49462 Nonbonded interactions: 122969 Sorted by model distance: nonbonded pdb=" O3 NAG A 614 " pdb=" O7 NAG A 614 " model vdw 2.188 2.440 nonbonded pdb=" O3 NAG I 2 " pdb=" O7 NAG I 2 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR C 240 " pdb=" O6 NAG C 602 " model vdw 2.413 2.440 nonbonded pdb=" C ASN A 195 " pdb=" OD1 ASN A 195 " model vdw 2.475 3.270 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.491 2.520 ... (remaining 122964 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 33 through 57 or resid 66 through 397 or resid 414 through \ 503 or resid 601 through 611)) selection = (chain 'C' and (resid 33 through 57 or resid 66 through 185 or resid 189 through \ 503 or resid 601 through 611)) selection = (chain 'E' and (resid 33 through 503 or resid 601 through 611)) } ncs_group { reference = (chain 'B' and (resid 521 through 662 or resid 702)) selection = (chain 'D' and (resid 521 through 662 or resid 702)) selection = (chain 'F' and (resid 521 through 662 or resid 701)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } ncs_group { reference = (chain 'H' and resid 16 through 114) selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'T' } 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.720 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 43.560 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.180 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.021 0.128 16174 Z= 1.340 Angle : 1.674 10.118 22001 Z= 1.091 Chirality : 0.136 0.845 2774 Planarity : 0.018 0.301 2718 Dihedral : 11.267 106.459 7011 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1709 helix: 0.16 (0.23), residues: 463 sheet: 1.04 (0.23), residues: 454 loop : 1.01 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.009 TRP C 35 HIS 0.008 0.002 HIS A 216 PHE 0.044 0.006 PHE A 383 TYR 0.031 0.006 TYR E 318 ARG 0.009 0.001 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8953 (ttm) cc_final: 0.8614 (tpp) REVERT: C 199 SER cc_start: 0.8873 (p) cc_final: 0.7733 (m) REVERT: C 349 LEU cc_start: 0.9538 (mt) cc_final: 0.9319 (mp) REVERT: C 368 ASP cc_start: 0.7771 (t70) cc_final: 0.7164 (p0) REVERT: C 376 PHE cc_start: 0.6707 (t80) cc_final: 0.6148 (t80) REVERT: C 435 TYR cc_start: 0.9063 (t80) cc_final: 0.8658 (t80) REVERT: C 450 THR cc_start: 0.9044 (p) cc_final: 0.8809 (p) REVERT: C 468 PHE cc_start: 0.8564 (m-80) cc_final: 0.8201 (m-80) REVERT: C 492 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8098 (mm-30) REVERT: D 548 ILE cc_start: 0.9194 (mt) cc_final: 0.8594 (mm) REVERT: D 590 GLN cc_start: 0.9365 (mm-40) cc_final: 0.9097 (tp40) REVERT: D 591 GLN cc_start: 0.8930 (tt0) cc_final: 0.8525 (tt0) REVERT: D 603 ILE cc_start: 0.9239 (mt) cc_final: 0.8818 (tt) REVERT: D 623 TRP cc_start: 0.8555 (m100) cc_final: 0.8323 (m100) REVERT: A 78 ASP cc_start: 0.8329 (t0) cc_final: 0.8040 (t0) REVERT: A 196 CYS cc_start: 0.8284 (m) cc_final: 0.7898 (m) REVERT: A 217 TYR cc_start: 0.9182 (m-80) cc_final: 0.8860 (m-80) REVERT: A 377 ASN cc_start: 0.8464 (t0) cc_final: 0.8244 (t0) REVERT: A 399 THR cc_start: 0.6395 (t) cc_final: 0.6073 (m) REVERT: B 565 LEU cc_start: 0.8369 (mt) cc_final: 0.7771 (tt) REVERT: B 590 GLN cc_start: 0.9353 (mm-40) cc_final: 0.9147 (tp40) REVERT: B 622 ILE cc_start: 0.8636 (mt) cc_final: 0.8247 (mt) REVERT: B 642 ILE cc_start: 0.9218 (mt) cc_final: 0.8585 (tt) REVERT: B 648 GLU cc_start: 0.8027 (tp30) cc_final: 0.7763 (tp30) REVERT: E 107 ASP cc_start: 0.8794 (m-30) cc_final: 0.8162 (t0) REVERT: E 295 ASN cc_start: 0.8395 (m-40) cc_final: 0.7628 (t0) REVERT: F 563 GLN cc_start: 0.8674 (pt0) cc_final: 0.8384 (pt0) REVERT: F 631 TRP cc_start: 0.8388 (t-100) cc_final: 0.8099 (t-100) REVERT: F 638 TYR cc_start: 0.8172 (m-80) cc_final: 0.7874 (m-10) REVERT: F 656 ASN cc_start: 0.8793 (m-40) cc_final: 0.8576 (m-40) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.2971 time to fit residues: 222.4088 Evaluate side-chains 286 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN D 551 GLN D 552 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS E 425 ASN F 552 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16174 Z= 0.230 Angle : 0.711 10.010 22001 Z= 0.366 Chirality : 0.049 0.306 2774 Planarity : 0.005 0.048 2718 Dihedral : 8.456 84.637 3716 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1709 helix: 0.86 (0.24), residues: 434 sheet: 0.74 (0.24), residues: 403 loop : 0.66 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 610 HIS 0.010 0.001 HIS C 72 PHE 0.023 0.003 PHE F 522 TYR 0.027 0.002 TYR D 638 ARG 0.004 0.001 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 ASN cc_start: 0.7993 (m-40) cc_final: 0.7552 (p0) REVERT: C 104 MET cc_start: 0.8988 (ttm) cc_final: 0.8632 (tpp) REVERT: C 112 TRP cc_start: 0.9021 (t-100) cc_final: 0.8585 (t-100) REVERT: C 122 LEU cc_start: 0.9176 (mp) cc_final: 0.8781 (tt) REVERT: C 180 ASP cc_start: 0.8315 (m-30) cc_final: 0.7833 (m-30) REVERT: C 259 LEU cc_start: 0.9560 (mp) cc_final: 0.9299 (mm) REVERT: C 340 GLU cc_start: 0.8494 (pt0) cc_final: 0.8205 (tp30) REVERT: C 468 PHE cc_start: 0.8248 (m-80) cc_final: 0.7813 (m-80) REVERT: C 484 TYR cc_start: 0.8559 (p90) cc_final: 0.8223 (p90) REVERT: C 492 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8120 (mm-30) REVERT: D 548 ILE cc_start: 0.9000 (mt) cc_final: 0.8541 (mm) REVERT: D 550 GLN cc_start: 0.8803 (mm-40) cc_final: 0.7827 (tm-30) REVERT: A 35 TRP cc_start: 0.8039 (m100) cc_final: 0.7434 (m100) REVERT: A 78 ASP cc_start: 0.8311 (t0) cc_final: 0.8084 (t70) REVERT: A 103 GLN cc_start: 0.8198 (tp40) cc_final: 0.7980 (tp40) REVERT: A 166 ARG cc_start: 0.8561 (tpp80) cc_final: 0.8334 (mmt180) REVERT: A 217 TYR cc_start: 0.8998 (m-80) cc_final: 0.8229 (m-80) REVERT: A 315 GLN cc_start: 0.8549 (mp10) cc_final: 0.8053 (mp10) REVERT: B 565 LEU cc_start: 0.8564 (mt) cc_final: 0.7687 (tt) REVERT: B 590 GLN cc_start: 0.9375 (mm-40) cc_final: 0.9159 (tp40) REVERT: B 631 TRP cc_start: 0.9003 (t-100) cc_final: 0.8786 (t-100) REVERT: B 642 ILE cc_start: 0.9245 (mt) cc_final: 0.8895 (tt) REVERT: B 643 TYR cc_start: 0.9149 (m-80) cc_final: 0.8913 (m-80) REVERT: E 103 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7394 (tm-30) REVERT: E 232 LYS cc_start: 0.8128 (mttp) cc_final: 0.7521 (tttt) REVERT: E 256 SER cc_start: 0.9188 (p) cc_final: 0.8945 (t) REVERT: E 430 ILE cc_start: 0.8622 (pt) cc_final: 0.8249 (mt) REVERT: E 474 ASP cc_start: 0.7488 (t0) cc_final: 0.6976 (m-30) REVERT: F 650 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8363 (tm-30) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.2826 time to fit residues: 151.2632 Evaluate side-chains 246 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 173 optimal weight: 0.0980 chunk 187 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 59 optimal weight: 0.0050 chunk 139 optimal weight: 10.0000 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN D 563 GLN D 630 GLN A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16174 Z= 0.183 Angle : 0.590 8.598 22001 Z= 0.304 Chirality : 0.046 0.276 2774 Planarity : 0.004 0.042 2718 Dihedral : 7.382 74.976 3716 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1709 helix: 0.81 (0.26), residues: 435 sheet: 0.70 (0.24), residues: 425 loop : 0.58 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 610 HIS 0.008 0.001 HIS E 105 PHE 0.024 0.002 PHE A 53 TYR 0.016 0.002 TYR E 173 ARG 0.009 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9006 (ttm) cc_final: 0.8451 (tpp) REVERT: C 112 TRP cc_start: 0.9005 (t-100) cc_final: 0.8764 (t-100) REVERT: C 122 LEU cc_start: 0.9195 (mp) cc_final: 0.8785 (tt) REVERT: C 180 ASP cc_start: 0.8245 (m-30) cc_final: 0.7664 (m-30) REVERT: C 340 GLU cc_start: 0.8455 (pt0) cc_final: 0.8083 (tp30) REVERT: C 468 PHE cc_start: 0.8190 (m-80) cc_final: 0.7825 (m-80) REVERT: C 484 TYR cc_start: 0.8367 (p90) cc_final: 0.7996 (p90) REVERT: C 491 ILE cc_start: 0.9098 (tp) cc_final: 0.8616 (mm) REVERT: C 492 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8055 (mm-30) REVERT: C 494 LEU cc_start: 0.8485 (tp) cc_final: 0.8059 (tp) REVERT: C 500 ARG cc_start: 0.2910 (ptt-90) cc_final: 0.2673 (ptt-90) REVERT: D 550 GLN cc_start: 0.8840 (mm-40) cc_final: 0.7901 (tm-30) REVERT: D 574 LYS cc_start: 0.9536 (mmtp) cc_final: 0.9232 (mmtm) REVERT: D 596 TRP cc_start: 0.8826 (m-10) cc_final: 0.7842 (m-10) REVERT: D 601 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8660 (mmmm) REVERT: D 603 ILE cc_start: 0.9164 (mt) cc_final: 0.8835 (tt) REVERT: D 643 TYR cc_start: 0.8629 (m-10) cc_final: 0.8261 (m-10) REVERT: A 35 TRP cc_start: 0.8061 (m100) cc_final: 0.7481 (m100) REVERT: A 78 ASP cc_start: 0.8380 (t0) cc_final: 0.8150 (t0) REVERT: A 217 TYR cc_start: 0.8965 (m-80) cc_final: 0.7937 (m-80) REVERT: A 315 GLN cc_start: 0.8781 (mp10) cc_final: 0.8229 (mp10) REVERT: A 492 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8367 (mt-10) REVERT: B 565 LEU cc_start: 0.8627 (mt) cc_final: 0.7725 (tp) REVERT: B 631 TRP cc_start: 0.9084 (t-100) cc_final: 0.8875 (t-100) REVERT: B 642 ILE cc_start: 0.9263 (mt) cc_final: 0.8837 (tt) REVERT: B 643 TYR cc_start: 0.9141 (m-80) cc_final: 0.8909 (m-80) REVERT: E 376 PHE cc_start: 0.8236 (t80) cc_final: 0.8029 (t80) REVERT: E 426 MET cc_start: 0.7599 (ttm) cc_final: 0.7061 (ttp) REVERT: E 430 ILE cc_start: 0.8731 (pt) cc_final: 0.8441 (mt) REVERT: E 474 ASP cc_start: 0.7606 (t0) cc_final: 0.7126 (m-30) REVERT: E 494 LEU cc_start: 0.9315 (tp) cc_final: 0.9080 (tp) REVERT: F 577 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7906 (tm-30) REVERT: F 616 ASN cc_start: 0.8080 (m-40) cc_final: 0.7696 (t0) REVERT: F 650 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8258 (tm-30) REVERT: F 657 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8432 (tm-30) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.2799 time to fit residues: 137.7412 Evaluate side-chains 238 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN A 85 HIS A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 374 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16174 Z= 0.367 Angle : 0.735 11.524 22001 Z= 0.369 Chirality : 0.049 0.293 2774 Planarity : 0.004 0.037 2718 Dihedral : 7.465 64.393 3716 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1709 helix: 0.49 (0.25), residues: 437 sheet: 0.67 (0.24), residues: 427 loop : 0.09 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 571 HIS 0.017 0.002 HIS C 72 PHE 0.022 0.003 PHE F 522 TYR 0.021 0.002 TYR F 586 ARG 0.013 0.001 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9074 (ttm) cc_final: 0.8397 (tpp) REVERT: C 112 TRP cc_start: 0.9011 (t-100) cc_final: 0.8651 (t-100) REVERT: C 122 LEU cc_start: 0.9212 (mp) cc_final: 0.8795 (tt) REVERT: C 180 ASP cc_start: 0.8496 (m-30) cc_final: 0.7827 (m-30) REVERT: C 340 GLU cc_start: 0.8486 (pt0) cc_final: 0.8078 (tm-30) REVERT: C 484 TYR cc_start: 0.8405 (p90) cc_final: 0.8105 (p90) REVERT: D 545 LEU cc_start: 0.9584 (mm) cc_final: 0.9348 (mm) REVERT: D 574 LYS cc_start: 0.9525 (mmtp) cc_final: 0.9267 (mmtm) REVERT: D 603 ILE cc_start: 0.9213 (mt) cc_final: 0.8769 (tt) REVERT: A 35 TRP cc_start: 0.8086 (m100) cc_final: 0.7480 (m100) REVERT: A 195 ASN cc_start: 0.9109 (p0) cc_final: 0.8878 (p0) REVERT: A 217 TYR cc_start: 0.9062 (m-80) cc_final: 0.7939 (m-80) REVERT: A 315 GLN cc_start: 0.8635 (mp10) cc_final: 0.8415 (mp10) REVERT: A 484 TYR cc_start: 0.9437 (p90) cc_final: 0.9170 (p90) REVERT: B 565 LEU cc_start: 0.8606 (mt) cc_final: 0.7588 (tp) REVERT: E 264 SER cc_start: 0.8611 (m) cc_final: 0.8118 (p) REVERT: E 426 MET cc_start: 0.7680 (ttm) cc_final: 0.7448 (ttp) REVERT: E 491 ILE cc_start: 0.9080 (mp) cc_final: 0.8864 (mt) REVERT: F 548 ILE cc_start: 0.8974 (mt) cc_final: 0.8646 (mm) REVERT: F 584 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8342 (mt-10) REVERT: F 642 ILE cc_start: 0.9426 (pt) cc_final: 0.9161 (pt) REVERT: F 658 GLN cc_start: 0.9226 (tp40) cc_final: 0.9000 (tp40) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2719 time to fit residues: 112.8497 Evaluate side-chains 210 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 137 optimal weight: 0.0060 chunk 76 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 46 optimal weight: 0.0030 overall best weight: 0.5608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN D 552 GLN D 651 ASN A 72 HIS A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN E 72 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16174 Z= 0.153 Angle : 0.557 8.858 22001 Z= 0.285 Chirality : 0.045 0.264 2774 Planarity : 0.004 0.036 2718 Dihedral : 6.492 60.018 3716 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1709 helix: 0.91 (0.26), residues: 425 sheet: 0.71 (0.24), residues: 432 loop : 0.13 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 571 HIS 0.005 0.001 HIS C 72 PHE 0.023 0.002 PHE A 53 TYR 0.019 0.001 TYR B 643 ARG 0.007 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9037 (ttm) cc_final: 0.8349 (tpp) REVERT: C 180 ASP cc_start: 0.8433 (m-30) cc_final: 0.7804 (m-30) REVERT: C 194 ILE cc_start: 0.9385 (tp) cc_final: 0.9159 (tp) REVERT: C 340 GLU cc_start: 0.8447 (pt0) cc_final: 0.8120 (tm-30) REVERT: C 484 TYR cc_start: 0.8388 (p90) cc_final: 0.8075 (p90) REVERT: C 494 LEU cc_start: 0.8496 (tp) cc_final: 0.8104 (tp) REVERT: D 571 TRP cc_start: 0.8815 (m-10) cc_final: 0.8599 (m-10) REVERT: D 574 LYS cc_start: 0.9497 (mmtp) cc_final: 0.9259 (mmtm) REVERT: D 596 TRP cc_start: 0.8856 (m-10) cc_final: 0.8106 (m-10) REVERT: D 603 ILE cc_start: 0.9082 (mt) cc_final: 0.8628 (tt) REVERT: D 642 ILE cc_start: 0.9160 (mt) cc_final: 0.8868 (tt) REVERT: D 643 TYR cc_start: 0.8752 (m-10) cc_final: 0.8363 (m-10) REVERT: A 35 TRP cc_start: 0.8017 (m100) cc_final: 0.6798 (m100) REVERT: A 85 HIS cc_start: 0.8475 (t-90) cc_final: 0.8237 (t-90) REVERT: A 173 TYR cc_start: 0.8751 (p90) cc_final: 0.8389 (p90) REVERT: A 315 GLN cc_start: 0.8741 (mp10) cc_final: 0.8398 (mp10) REVERT: A 494 LEU cc_start: 0.9275 (mm) cc_final: 0.8901 (mm) REVERT: A 502 LYS cc_start: 0.8232 (tmmt) cc_final: 0.7865 (tttm) REVERT: B 565 LEU cc_start: 0.8544 (mt) cc_final: 0.7585 (tp) REVERT: B 648 GLU cc_start: 0.8539 (tp30) cc_final: 0.8315 (tp30) REVERT: E 103 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8403 (tm-30) REVERT: E 426 MET cc_start: 0.7615 (ttm) cc_final: 0.7283 (ttp) REVERT: F 548 ILE cc_start: 0.8969 (mt) cc_final: 0.8677 (mm) REVERT: F 574 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8869 (ttpt) REVERT: F 577 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8138 (tm-30) REVERT: F 603 ILE cc_start: 0.8286 (pt) cc_final: 0.8013 (tt) REVERT: F 642 ILE cc_start: 0.9440 (pt) cc_final: 0.9151 (pt) REVERT: F 658 GLN cc_start: 0.9225 (tp40) cc_final: 0.8979 (tp40) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2730 time to fit residues: 118.1213 Evaluate side-chains 224 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS C 170 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 16174 Z= 0.579 Angle : 0.922 8.693 22001 Z= 0.455 Chirality : 0.054 0.305 2774 Planarity : 0.005 0.045 2718 Dihedral : 8.377 58.900 3716 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1709 helix: 0.12 (0.25), residues: 441 sheet: 0.21 (0.24), residues: 425 loop : -0.31 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP E 45 HIS 0.013 0.003 HIS C 374 PHE 0.024 0.004 PHE C 383 TYR 0.028 0.003 TYR A 217 ARG 0.007 0.001 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9187 (ttm) cc_final: 0.8736 (tpp) REVERT: C 180 ASP cc_start: 0.8651 (m-30) cc_final: 0.8074 (m-30) REVERT: C 340 GLU cc_start: 0.8583 (pt0) cc_final: 0.8140 (tm-30) REVERT: C 484 TYR cc_start: 0.8489 (p90) cc_final: 0.8184 (p90) REVERT: D 574 LYS cc_start: 0.9550 (mmtp) cc_final: 0.9208 (mmtm) REVERT: D 584 GLU cc_start: 0.9022 (pp20) cc_final: 0.8786 (pp20) REVERT: D 603 ILE cc_start: 0.9205 (mt) cc_final: 0.8667 (tt) REVERT: D 642 ILE cc_start: 0.9272 (mt) cc_final: 0.8985 (tt) REVERT: A 173 TYR cc_start: 0.8802 (p90) cc_final: 0.8434 (p90) REVERT: A 195 ASN cc_start: 0.9289 (p0) cc_final: 0.9083 (p0) REVERT: A 502 LYS cc_start: 0.8316 (tmmt) cc_final: 0.7966 (tttt) REVERT: B 565 LEU cc_start: 0.8679 (mt) cc_final: 0.7601 (tp) REVERT: E 103 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8546 (tm-30) REVERT: E 426 MET cc_start: 0.7753 (ttm) cc_final: 0.7253 (ttt) REVERT: F 548 ILE cc_start: 0.9100 (mt) cc_final: 0.8821 (mm) REVERT: F 603 ILE cc_start: 0.8300 (pt) cc_final: 0.8043 (tt) REVERT: F 642 ILE cc_start: 0.9529 (pt) cc_final: 0.9273 (pt) REVERT: F 653 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8642 (tp-100) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.2997 time to fit residues: 107.8099 Evaluate side-chains 190 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 104 optimal weight: 0.2980 chunk 155 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 348 GLN D 552 GLN D 554 ASN A 72 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN E 72 HIS E 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16174 Z= 0.165 Angle : 0.584 8.157 22001 Z= 0.297 Chirality : 0.045 0.286 2774 Planarity : 0.004 0.044 2718 Dihedral : 6.878 53.303 3716 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1709 helix: 0.58 (0.25), residues: 443 sheet: 0.37 (0.24), residues: 433 loop : -0.13 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 571 HIS 0.005 0.001 HIS C 72 PHE 0.023 0.002 PHE D 522 TYR 0.012 0.001 TYR D 638 ARG 0.007 0.001 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 ASP cc_start: 0.8548 (m-30) cc_final: 0.7960 (m-30) REVERT: C 194 ILE cc_start: 0.9426 (tp) cc_final: 0.9191 (tp) REVERT: C 252 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8449 (mtmt) REVERT: C 340 GLU cc_start: 0.8474 (pt0) cc_final: 0.8041 (tm-30) REVERT: C 494 LEU cc_start: 0.8883 (tp) cc_final: 0.8385 (tp) REVERT: D 542 ARG cc_start: 0.9158 (ttp-110) cc_final: 0.8843 (ttp80) REVERT: D 574 LYS cc_start: 0.9502 (mmtp) cc_final: 0.9251 (mmtm) REVERT: D 603 ILE cc_start: 0.9112 (mt) cc_final: 0.8552 (tt) REVERT: D 643 TYR cc_start: 0.8804 (m-10) cc_final: 0.8352 (m-10) REVERT: A 173 TYR cc_start: 0.8720 (p90) cc_final: 0.8459 (p90) REVERT: A 195 ASN cc_start: 0.9057 (p0) cc_final: 0.8831 (p0) REVERT: A 217 TYR cc_start: 0.8990 (m-80) cc_final: 0.7851 (m-80) REVERT: A 426 MET cc_start: 0.7850 (ttm) cc_final: 0.7297 (ttp) REVERT: B 530 MET cc_start: 0.8596 (mtp) cc_final: 0.8377 (mtp) REVERT: B 565 LEU cc_start: 0.8557 (mt) cc_final: 0.7555 (tp) REVERT: E 103 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8217 (tm-30) REVERT: E 426 MET cc_start: 0.7439 (ttm) cc_final: 0.6952 (ttt) REVERT: F 577 GLN cc_start: 0.8608 (tm130) cc_final: 0.8240 (tm-30) REVERT: F 603 ILE cc_start: 0.8335 (pt) cc_final: 0.8103 (tt) REVERT: F 642 ILE cc_start: 0.9467 (pt) cc_final: 0.9173 (pt) REVERT: F 643 TYR cc_start: 0.8940 (m-10) cc_final: 0.8690 (m-80) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2698 time to fit residues: 109.9600 Evaluate side-chains 203 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.0270 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.0070 chunk 117 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 554 ASN A 72 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16174 Z= 0.151 Angle : 0.555 10.347 22001 Z= 0.283 Chirality : 0.045 0.322 2774 Planarity : 0.004 0.039 2718 Dihedral : 6.299 56.097 3716 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.33 (0.20), residues: 1709 helix: 0.87 (0.26), residues: 430 sheet: 0.51 (0.25), residues: 433 loop : -0.18 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 571 HIS 0.004 0.001 HIS A 374 PHE 0.027 0.002 PHE A 53 TYR 0.019 0.001 TYR E 191 ARG 0.008 0.001 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9073 (ttm) cc_final: 0.8814 (ttm) REVERT: C 180 ASP cc_start: 0.8486 (m-30) cc_final: 0.7991 (m-30) REVERT: C 194 ILE cc_start: 0.9339 (tp) cc_final: 0.9114 (tp) REVERT: C 252 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8451 (mtmt) REVERT: D 542 ARG cc_start: 0.9128 (ttp-110) cc_final: 0.8927 (ttp80) REVERT: D 574 LYS cc_start: 0.9524 (mmtp) cc_final: 0.9253 (mmtm) REVERT: D 603 ILE cc_start: 0.9054 (mt) cc_final: 0.8433 (tt) REVERT: D 643 TYR cc_start: 0.8749 (m-10) cc_final: 0.8265 (m-10) REVERT: A 112 TRP cc_start: 0.9154 (t-100) cc_final: 0.8766 (t-100) REVERT: A 173 TYR cc_start: 0.8705 (p90) cc_final: 0.8456 (p90) REVERT: A 180 ASP cc_start: 0.8882 (m-30) cc_final: 0.8509 (m-30) REVERT: A 217 TYR cc_start: 0.8895 (m-80) cc_final: 0.7720 (m-80) REVERT: A 315 GLN cc_start: 0.8889 (mp10) cc_final: 0.8669 (mp10) REVERT: B 565 LEU cc_start: 0.8520 (mt) cc_final: 0.7517 (tp) REVERT: B 617 ARG cc_start: 0.8053 (mtp-110) cc_final: 0.7760 (ttm-80) REVERT: B 631 TRP cc_start: 0.8987 (t-100) cc_final: 0.8727 (t-100) REVERT: E 103 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8593 (tm-30) REVERT: E 426 MET cc_start: 0.7231 (ttm) cc_final: 0.6727 (ttt) REVERT: F 603 ILE cc_start: 0.8277 (pt) cc_final: 0.8075 (tt) REVERT: F 642 ILE cc_start: 0.9460 (pt) cc_final: 0.9187 (pt) REVERT: F 643 TYR cc_start: 0.8830 (m-10) cc_final: 0.8582 (m-80) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2742 time to fit residues: 105.5525 Evaluate side-chains 206 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 134 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16174 Z= 0.185 Angle : 0.547 6.682 22001 Z= 0.281 Chirality : 0.045 0.413 2774 Planarity : 0.004 0.040 2718 Dihedral : 6.097 54.250 3716 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.37 (0.20), residues: 1709 helix: 0.95 (0.26), residues: 430 sheet: 0.49 (0.25), residues: 445 loop : -0.17 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 571 HIS 0.005 0.001 HIS C 72 PHE 0.025 0.002 PHE A 53 TYR 0.015 0.001 TYR D 586 ARG 0.006 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9038 (ttm) cc_final: 0.8825 (ttm) REVERT: C 180 ASP cc_start: 0.8372 (m-30) cc_final: 0.7765 (m-30) REVERT: C 252 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8436 (mtmt) REVERT: D 542 ARG cc_start: 0.9193 (ttp-110) cc_final: 0.8887 (ttp80) REVERT: D 574 LYS cc_start: 0.9527 (mmtp) cc_final: 0.9255 (mmtm) REVERT: D 603 ILE cc_start: 0.9077 (mt) cc_final: 0.8425 (tt) REVERT: D 609 PRO cc_start: 0.7891 (Cg_exo) cc_final: 0.7561 (Cg_endo) REVERT: D 643 TYR cc_start: 0.8726 (m-10) cc_final: 0.8270 (m-10) REVERT: A 53 PHE cc_start: 0.9441 (p90) cc_final: 0.9222 (p90) REVERT: A 112 TRP cc_start: 0.9174 (t-100) cc_final: 0.8914 (t-100) REVERT: A 180 ASP cc_start: 0.8943 (m-30) cc_final: 0.8699 (m-30) REVERT: A 195 ASN cc_start: 0.9019 (p0) cc_final: 0.8813 (p0) REVERT: A 217 TYR cc_start: 0.8884 (m-80) cc_final: 0.7670 (m-80) REVERT: A 315 GLN cc_start: 0.8879 (mp10) cc_final: 0.8662 (mp10) REVERT: A 492 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8503 (mt-10) REVERT: B 565 LEU cc_start: 0.8543 (mt) cc_final: 0.7476 (tp) REVERT: B 631 TRP cc_start: 0.8990 (t-100) cc_final: 0.8736 (t-100) REVERT: B 633 LYS cc_start: 0.9310 (tppt) cc_final: 0.9087 (ttmm) REVERT: E 103 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8685 (tm-30) REVERT: E 426 MET cc_start: 0.7325 (ttm) cc_final: 0.6867 (ttt) REVERT: F 577 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8388 (tm-30) REVERT: F 603 ILE cc_start: 0.8291 (pt) cc_final: 0.8087 (tt) REVERT: F 642 ILE cc_start: 0.9471 (pt) cc_final: 0.9175 (pt) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2698 time to fit residues: 104.2464 Evaluate side-chains 199 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.9990 chunk 181 optimal weight: 0.0470 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16174 Z= 0.262 Angle : 0.601 8.173 22001 Z= 0.309 Chirality : 0.046 0.308 2774 Planarity : 0.004 0.044 2718 Dihedral : 6.309 53.772 3716 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % 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 (0.20), residues: 1709 helix: 0.93 (0.26), residues: 429 sheet: 0.47 (0.25), residues: 444 loop : -0.24 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 571 HIS 0.005 0.001 HIS C 72 PHE 0.023 0.002 PHE A 53 TYR 0.036 0.002 TYR F 586 ARG 0.007 0.001 ARG F 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9087 (ttm) cc_final: 0.8779 (ttm) REVERT: C 180 ASP cc_start: 0.8441 (m-30) cc_final: 0.7858 (m-30) REVERT: C 252 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8424 (mtmt) REVERT: C 340 GLU cc_start: 0.8482 (pt0) cc_final: 0.8091 (tm-30) REVERT: D 542 ARG cc_start: 0.9147 (ttp-110) cc_final: 0.8298 (ttp-170) REVERT: D 552 GLN cc_start: 0.8481 (tp40) cc_final: 0.8280 (tp40) REVERT: D 574 LYS cc_start: 0.9532 (mmtp) cc_final: 0.9253 (mmtm) REVERT: D 603 ILE cc_start: 0.9127 (mt) cc_final: 0.8486 (tt) REVERT: D 609 PRO cc_start: 0.8440 (Cg_exo) cc_final: 0.8082 (Cg_endo) REVERT: D 643 TYR cc_start: 0.8701 (m-10) cc_final: 0.8343 (m-10) REVERT: A 180 ASP cc_start: 0.9015 (m-30) cc_final: 0.8754 (m-30) REVERT: A 195 ASN cc_start: 0.9106 (p0) cc_final: 0.8826 (p0) REVERT: A 217 TYR cc_start: 0.8877 (m-80) cc_final: 0.7730 (m-80) REVERT: A 426 MET cc_start: 0.7648 (ttm) cc_final: 0.7094 (ttp) REVERT: A 492 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8563 (mt-10) REVERT: B 565 LEU cc_start: 0.8524 (mt) cc_final: 0.7444 (tp) REVERT: B 631 TRP cc_start: 0.8996 (t-100) cc_final: 0.8753 (t-100) REVERT: B 633 LYS cc_start: 0.9315 (tppt) cc_final: 0.9056 (ttmm) REVERT: E 103 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8705 (tm-30) REVERT: E 426 MET cc_start: 0.7268 (ttm) cc_final: 0.6837 (ttt) REVERT: F 577 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8425 (tm-30) REVERT: F 603 ILE cc_start: 0.8404 (pt) cc_final: 0.8139 (tt) REVERT: F 642 ILE cc_start: 0.9528 (pt) cc_final: 0.9203 (pt) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2746 time to fit residues: 104.0472 Evaluate side-chains 202 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 46 optimal weight: 0.0980 chunk 139 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.080598 restraints weight = 45108.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.082563 restraints weight = 28510.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.083899 restraints weight = 20717.541| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16174 Z= 0.214 Angle : 0.565 8.830 22001 Z= 0.292 Chirality : 0.045 0.338 2774 Planarity : 0.004 0.045 2718 Dihedral : 6.122 53.548 3716 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % 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 (0.20), residues: 1709 helix: 0.94 (0.26), residues: 429 sheet: 0.48 (0.24), residues: 444 loop : -0.24 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 571 HIS 0.005 0.001 HIS C 72 PHE 0.023 0.002 PHE A 53 TYR 0.018 0.001 TYR F 643 ARG 0.006 0.001 ARG B 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3269.75 seconds wall clock time: 59 minutes 47.23 seconds (3587.23 seconds total)