Starting phenix.real_space_refine on Sun Feb 25 03:36:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/02_2024/7k08_22589.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/02_2024/7k08_22589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/02_2024/7k08_22589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/02_2024/7k08_22589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/02_2024/7k08_22589.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/02_2024/7k08_22589.pdb" } resolution = 4.7 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: 5 Type Number sf(0) Gaussians S 63 5.16 5 C 15426 2.51 5 N 4032 2.21 5 O 4608 1.98 5 H 24606 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48735 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5415 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 318} Chain: "B" Number of atoms: 5415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5415 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 318} Chain: "C" Number of atoms: 5415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5415 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 318} Chain: "D" Number of atoms: 5415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5415 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 318} Chain: "E" Number of atoms: 5415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5415 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 318} Chain: "F" Number of atoms: 5415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5415 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 318} Chain: "G" Number of atoms: 5415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5415 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 318} Chain: "H" Number of atoms: 5415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5415 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 318} Chain: "I" Number of atoms: 5415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5415 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 318} Time building chain proxies: 20.21, per 1000 atoms: 0.41 Number of scatterers: 48735 At special positions: 0 Unit cell: (178.92, 178.92, 74.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 O 4608 8.00 N 4032 7.00 C 15426 6.00 H 24606 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.62 Conformation dependent library (CDL) restraints added in 4.6 seconds 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5688 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 27 sheets defined 52.1% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 363 through 382 removed outlier: 3.602A pdb=" N THR A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 457 No H-bonds generated for 'chain 'A' and resid 456 through 457' Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 464 through 478 Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 512 through 525 removed outlier: 4.252A pdb=" N LYS A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 533 through 548 removed outlier: 3.629A pdb=" N ILE A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 562 removed outlier: 4.986A pdb=" N VAL A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 572 through 575 Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.562A pdb=" N GLU A 587 " --> pdb=" O GLY A 583 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A 589 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 606 through 619 Processing helix chain 'A' and resid 635 through 645 Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'B' and resid 363 through 382 removed outlier: 3.601A pdb=" N THR B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 457 No H-bonds generated for 'chain 'B' and resid 456 through 457' Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 464 through 478 Processing helix chain 'B' and resid 486 through 494 Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'B' and resid 502 through 512 Processing helix chain 'B' and resid 512 through 525 removed outlier: 4.252A pdb=" N LYS B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 533 through 548 removed outlier: 3.629A pdb=" N ILE B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 543 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 562 removed outlier: 4.986A pdb=" N VAL B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 571 Processing helix chain 'B' and resid 572 through 575 Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.564A pdb=" N GLU B 587 " --> pdb=" O GLY B 583 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 606 through 619 Processing helix chain 'B' and resid 635 through 645 Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'C' and resid 363 through 382 removed outlier: 3.601A pdb=" N THR C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 457 No H-bonds generated for 'chain 'C' and resid 456 through 457' Processing helix chain 'C' and resid 458 through 462 Processing helix chain 'C' and resid 464 through 478 Processing helix chain 'C' and resid 486 through 494 Processing helix chain 'C' and resid 497 through 501 Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 512 through 525 removed outlier: 4.252A pdb=" N LYS C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 528 No H-bonds generated for 'chain 'C' and resid 526 through 528' Processing helix chain 'C' and resid 533 through 548 removed outlier: 3.629A pdb=" N ILE C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE C 543 " --> pdb=" O GLU C 539 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR C 546 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 562 removed outlier: 4.986A pdb=" N VAL C 558 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 571 Processing helix chain 'C' and resid 572 through 575 Processing helix chain 'C' and resid 583 through 591 removed outlier: 3.563A pdb=" N GLU C 587 " --> pdb=" O GLY C 583 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU C 589 " --> pdb=" O ASP C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 606 through 619 Processing helix chain 'C' and resid 635 through 645 Processing helix chain 'C' and resid 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' Processing helix chain 'D' and resid 363 through 382 removed outlier: 3.602A pdb=" N THR D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 457 No H-bonds generated for 'chain 'D' and resid 456 through 457' Processing helix chain 'D' and resid 458 through 462 Processing helix chain 'D' and resid 464 through 478 Processing helix chain 'D' and resid 486 through 494 Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'D' and resid 502 through 512 Processing helix chain 'D' and resid 512 through 525 removed outlier: 4.252A pdb=" N LYS D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 528 No H-bonds generated for 'chain 'D' and resid 526 through 528' Processing helix chain 'D' and resid 533 through 548 removed outlier: 3.629A pdb=" N ILE D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE D 543 " --> pdb=" O GLU D 539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR D 546 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 547 " --> pdb=" O PHE D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 562 removed outlier: 4.986A pdb=" N VAL D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 571 Processing helix chain 'D' and resid 572 through 575 Processing helix chain 'D' and resid 583 through 591 removed outlier: 3.563A pdb=" N GLU D 587 " --> pdb=" O GLY D 583 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU D 589 " --> pdb=" O ASP D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'D' and resid 606 through 619 Processing helix chain 'D' and resid 635 through 645 Processing helix chain 'D' and resid 656 through 658 No H-bonds generated for 'chain 'D' and resid 656 through 658' Processing helix chain 'E' and resid 363 through 382 removed outlier: 3.601A pdb=" N THR E 367 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 455 Processing helix chain 'E' and resid 456 through 457 No H-bonds generated for 'chain 'E' and resid 456 through 457' Processing helix chain 'E' and resid 458 through 462 Processing helix chain 'E' and resid 464 through 478 Processing helix chain 'E' and resid 486 through 494 Processing helix chain 'E' and resid 497 through 501 Processing helix chain 'E' and resid 502 through 512 Processing helix chain 'E' and resid 512 through 525 removed outlier: 4.252A pdb=" N LYS E 516 " --> pdb=" O LEU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 528 No H-bonds generated for 'chain 'E' and resid 526 through 528' Processing helix chain 'E' and resid 533 through 548 removed outlier: 3.630A pdb=" N ILE E 537 " --> pdb=" O ASP E 533 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE E 543 " --> pdb=" O GLU E 539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR E 546 " --> pdb=" O ILE E 542 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS E 547 " --> pdb=" O PHE E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 562 removed outlier: 4.987A pdb=" N VAL E 558 " --> pdb=" O LEU E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 571 Processing helix chain 'E' and resid 572 through 575 Processing helix chain 'E' and resid 583 through 591 removed outlier: 3.563A pdb=" N GLU E 587 " --> pdb=" O GLY E 583 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU E 589 " --> pdb=" O ASP E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'E' and resid 606 through 619 Processing helix chain 'E' and resid 635 through 645 Processing helix chain 'E' and resid 656 through 658 No H-bonds generated for 'chain 'E' and resid 656 through 658' Processing helix chain 'F' and resid 363 through 382 removed outlier: 3.601A pdb=" N THR F 367 " --> pdb=" O SER F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 455 Processing helix chain 'F' and resid 456 through 457 No H-bonds generated for 'chain 'F' and resid 456 through 457' Processing helix chain 'F' and resid 458 through 462 Processing helix chain 'F' and resid 464 through 478 Processing helix chain 'F' and resid 486 through 494 Processing helix chain 'F' and resid 497 through 501 Processing helix chain 'F' and resid 502 through 512 Processing helix chain 'F' and resid 512 through 525 removed outlier: 4.252A pdb=" N LYS F 516 " --> pdb=" O LEU F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 528 No H-bonds generated for 'chain 'F' and resid 526 through 528' Processing helix chain 'F' and resid 533 through 548 removed outlier: 3.630A pdb=" N ILE F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE F 543 " --> pdb=" O GLU F 539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR F 546 " --> pdb=" O ILE F 542 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS F 547 " --> pdb=" O PHE F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 562 removed outlier: 4.986A pdb=" N VAL F 558 " --> pdb=" O LEU F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 571 Processing helix chain 'F' and resid 572 through 575 Processing helix chain 'F' and resid 583 through 591 removed outlier: 3.563A pdb=" N GLU F 587 " --> pdb=" O GLY F 583 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU F 589 " --> pdb=" O ASP F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'F' and resid 606 through 619 Processing helix chain 'F' and resid 635 through 645 Processing helix chain 'F' and resid 656 through 658 No H-bonds generated for 'chain 'F' and resid 656 through 658' Processing helix chain 'G' and resid 363 through 382 removed outlier: 3.602A pdb=" N THR G 367 " --> pdb=" O SER G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 455 Processing helix chain 'G' and resid 456 through 457 No H-bonds generated for 'chain 'G' and resid 456 through 457' Processing helix chain 'G' and resid 458 through 462 Processing helix chain 'G' and resid 464 through 478 Processing helix chain 'G' and resid 486 through 494 Processing helix chain 'G' and resid 497 through 501 Processing helix chain 'G' and resid 502 through 512 Processing helix chain 'G' and resid 512 through 525 removed outlier: 4.252A pdb=" N LYS G 516 " --> pdb=" O LEU G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 528 No H-bonds generated for 'chain 'G' and resid 526 through 528' Processing helix chain 'G' and resid 533 through 548 removed outlier: 3.630A pdb=" N ILE G 537 " --> pdb=" O ASP G 533 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE G 543 " --> pdb=" O GLU G 539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR G 546 " --> pdb=" O ILE G 542 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS G 547 " --> pdb=" O PHE G 543 " (cutoff:3.500A) Processing helix chain 'G' and resid 552 through 562 removed outlier: 4.986A pdb=" N VAL G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 571 Processing helix chain 'G' and resid 572 through 575 Processing helix chain 'G' and resid 583 through 591 removed outlier: 3.563A pdb=" N GLU G 587 " --> pdb=" O GLY G 583 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU G 589 " --> pdb=" O ASP G 585 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing helix chain 'G' and resid 606 through 619 Processing helix chain 'G' and resid 635 through 645 Processing helix chain 'G' and resid 656 through 658 No H-bonds generated for 'chain 'G' and resid 656 through 658' Processing helix chain 'H' and resid 363 through 382 removed outlier: 3.602A pdb=" N THR H 367 " --> pdb=" O SER H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 455 Processing helix chain 'H' and resid 456 through 457 No H-bonds generated for 'chain 'H' and resid 456 through 457' Processing helix chain 'H' and resid 458 through 462 Processing helix chain 'H' and resid 464 through 478 Processing helix chain 'H' and resid 486 through 494 Processing helix chain 'H' and resid 497 through 501 Processing helix chain 'H' and resid 502 through 512 Processing helix chain 'H' and resid 512 through 525 removed outlier: 4.252A pdb=" N LYS H 516 " --> pdb=" O LEU H 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 528 No H-bonds generated for 'chain 'H' and resid 526 through 528' Processing helix chain 'H' and resid 533 through 548 removed outlier: 3.630A pdb=" N ILE H 537 " --> pdb=" O ASP H 533 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE H 543 " --> pdb=" O GLU H 539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR H 546 " --> pdb=" O ILE H 542 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS H 547 " --> pdb=" O PHE H 543 " (cutoff:3.500A) Processing helix chain 'H' and resid 552 through 562 removed outlier: 4.986A pdb=" N VAL H 558 " --> pdb=" O LEU H 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 571 Processing helix chain 'H' and resid 572 through 575 Processing helix chain 'H' and resid 583 through 591 removed outlier: 3.563A pdb=" N GLU H 587 " --> pdb=" O GLY H 583 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU H 589 " --> pdb=" O ASP H 585 " (cutoff:3.500A) Processing helix chain 'H' and resid 599 through 603 Processing helix chain 'H' and resid 606 through 619 Processing helix chain 'H' and resid 635 through 645 Processing helix chain 'H' and resid 656 through 658 No H-bonds generated for 'chain 'H' and resid 656 through 658' Processing helix chain 'I' and resid 363 through 382 removed outlier: 3.601A pdb=" N THR I 367 " --> pdb=" O SER I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 455 Processing helix chain 'I' and resid 456 through 457 No H-bonds generated for 'chain 'I' and resid 456 through 457' Processing helix chain 'I' and resid 458 through 462 Processing helix chain 'I' and resid 464 through 478 Processing helix chain 'I' and resid 486 through 494 Processing helix chain 'I' and resid 497 through 501 Processing helix chain 'I' and resid 502 through 512 Processing helix chain 'I' and resid 512 through 525 removed outlier: 4.253A pdb=" N LYS I 516 " --> pdb=" O LEU I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 528 No H-bonds generated for 'chain 'I' and resid 526 through 528' Processing helix chain 'I' and resid 533 through 548 removed outlier: 3.629A pdb=" N ILE I 537 " --> pdb=" O ASP I 533 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE I 543 " --> pdb=" O GLU I 539 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR I 546 " --> pdb=" O ILE I 542 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS I 547 " --> pdb=" O PHE I 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 552 through 562 removed outlier: 4.987A pdb=" N VAL I 558 " --> pdb=" O LEU I 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 571 Processing helix chain 'I' and resid 572 through 575 Processing helix chain 'I' and resid 583 through 591 removed outlier: 3.563A pdb=" N GLU I 587 " --> pdb=" O GLY I 583 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU I 589 " --> pdb=" O ASP I 585 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 603 Processing helix chain 'I' and resid 606 through 619 Processing helix chain 'I' and resid 635 through 645 Processing helix chain 'I' and resid 656 through 658 No H-bonds generated for 'chain 'I' and resid 656 through 658' Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.631A pdb=" N PHE A 402 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 654 removed outlier: 5.522A pdb=" N ILE A 629 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 630 " --> pdb=" O ASN A 578 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TRP A 580 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU A 577 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 667 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 579 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR A 669 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A 581 " --> pdb=" O THR A 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 389 through 390 removed outlier: 6.632A pdb=" N PHE B 402 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AA6, first strand: chain 'B' and resid 652 through 654 removed outlier: 5.522A pdb=" N ILE B 629 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 630 " --> pdb=" O ASN B 578 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TRP B 580 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU B 577 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU B 667 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 579 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR B 669 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU B 581 " --> pdb=" O THR B 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 389 through 390 removed outlier: 6.632A pdb=" N PHE C 402 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 418 through 420 Processing sheet with id=AA9, first strand: chain 'C' and resid 652 through 654 removed outlier: 5.521A pdb=" N ILE C 629 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 630 " --> pdb=" O ASN C 578 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TRP C 580 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU C 577 " --> pdb=" O LYS C 665 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU C 667 " --> pdb=" O LEU C 577 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 579 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR C 669 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU C 581 " --> pdb=" O THR C 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 389 through 390 removed outlier: 6.631A pdb=" N PHE D 402 " --> pdb=" O ILE D 409 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AB3, first strand: chain 'D' and resid 652 through 654 removed outlier: 5.522A pdb=" N ILE D 629 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU D 630 " --> pdb=" O ASN D 578 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TRP D 580 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU D 577 " --> pdb=" O LYS D 665 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU D 667 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL D 579 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR D 669 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU D 581 " --> pdb=" O THR D 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 389 through 390 removed outlier: 6.632A pdb=" N PHE E 402 " --> pdb=" O ILE E 409 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 418 through 420 Processing sheet with id=AB6, first strand: chain 'E' and resid 652 through 654 removed outlier: 5.522A pdb=" N ILE E 629 " --> pdb=" O LEU E 653 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU E 630 " --> pdb=" O ASN E 578 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TRP E 580 " --> pdb=" O LEU E 630 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU E 577 " --> pdb=" O LYS E 665 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU E 667 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL E 579 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR E 669 " --> pdb=" O VAL E 579 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU E 581 " --> pdb=" O THR E 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 389 through 390 removed outlier: 6.632A pdb=" N PHE F 402 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 418 through 420 Processing sheet with id=AB9, first strand: chain 'F' and resid 652 through 654 removed outlier: 5.521A pdb=" N ILE F 629 " --> pdb=" O LEU F 653 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU F 630 " --> pdb=" O ASN F 578 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TRP F 580 " --> pdb=" O LEU F 630 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU F 577 " --> pdb=" O LYS F 665 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU F 667 " --> pdb=" O LEU F 577 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL F 579 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR F 669 " --> pdb=" O VAL F 579 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU F 581 " --> pdb=" O THR F 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 389 through 390 removed outlier: 6.633A pdb=" N PHE G 402 " --> pdb=" O ILE G 409 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 418 through 420 Processing sheet with id=AC3, first strand: chain 'G' and resid 652 through 654 removed outlier: 5.521A pdb=" N ILE G 629 " --> pdb=" O LEU G 653 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU G 630 " --> pdb=" O ASN G 578 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TRP G 580 " --> pdb=" O LEU G 630 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU G 577 " --> pdb=" O LYS G 665 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU G 667 " --> pdb=" O LEU G 577 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL G 579 " --> pdb=" O LEU G 667 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR G 669 " --> pdb=" O VAL G 579 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU G 581 " --> pdb=" O THR G 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 389 through 390 removed outlier: 6.632A pdb=" N PHE H 402 " --> pdb=" O ILE H 409 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 418 through 420 Processing sheet with id=AC6, first strand: chain 'H' and resid 652 through 654 removed outlier: 5.522A pdb=" N ILE H 629 " --> pdb=" O LEU H 653 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU H 630 " --> pdb=" O ASN H 578 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TRP H 580 " --> pdb=" O LEU H 630 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU H 577 " --> pdb=" O LYS H 665 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU H 667 " --> pdb=" O LEU H 577 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL H 579 " --> pdb=" O LEU H 667 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR H 669 " --> pdb=" O VAL H 579 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU H 581 " --> pdb=" O THR H 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 389 through 390 removed outlier: 6.633A pdb=" N PHE I 402 " --> pdb=" O ILE I 409 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 418 through 420 Processing sheet with id=AC9, first strand: chain 'I' and resid 652 through 654 removed outlier: 5.522A pdb=" N ILE I 629 " --> pdb=" O LEU I 653 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU I 630 " --> pdb=" O ASN I 578 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TRP I 580 " --> pdb=" O LEU I 630 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU I 577 " --> pdb=" O LYS I 665 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU I 667 " --> pdb=" O LEU I 577 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL I 579 " --> pdb=" O LEU I 667 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR I 669 " --> pdb=" O VAL I 579 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU I 581 " --> pdb=" O THR I 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 998 hydrogen bonds defined for protein. 2724 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: 19.50 Time building geometry restraints manager: 42.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 24597 1.13 - 1.30: 4587 1.30 - 1.48: 9856 1.48 - 1.66: 9965 1.66 - 1.83: 117 Bond restraints: 49122 Sorted by residual: bond pdb=" NH2 ARG B 523 " pdb="HH21 ARG B 523 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" NH2 ARG G 523 " pdb="HH21 ARG G 523 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" NH2 ARG I 523 " pdb="HH21 ARG I 523 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.88e+01 bond pdb=" NH1 ARG G 609 " pdb="HH12 ARG G 609 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.88e+01 bond pdb=" NH1 ARG E 609 " pdb="HH12 ARG E 609 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.86e+01 ... (remaining 49117 not shown) Histogram of bond angle deviations from ideal: 74.97 - 90.47: 18 90.47 - 105.96: 1727 105.96 - 121.45: 79878 121.45 - 136.95: 7387 136.95 - 152.44: 9 Bond angle restraints: 89019 Sorted by residual: angle pdb=" C ARG B 532 " pdb=" N ASP B 533 " pdb=" CA ASP B 533 " ideal model delta sigma weight residual 122.62 152.44 -29.82 1.63e+00 3.76e-01 3.35e+02 angle pdb=" C ARG C 532 " pdb=" N ASP C 533 " pdb=" CA ASP C 533 " ideal model delta sigma weight residual 122.62 152.43 -29.81 1.63e+00 3.76e-01 3.34e+02 angle pdb=" C ARG I 532 " pdb=" N ASP I 533 " pdb=" CA ASP I 533 " ideal model delta sigma weight residual 122.62 152.41 -29.79 1.63e+00 3.76e-01 3.34e+02 angle pdb=" C ARG G 532 " pdb=" N ASP G 533 " pdb=" CA ASP G 533 " ideal model delta sigma weight residual 122.62 152.41 -29.79 1.63e+00 3.76e-01 3.34e+02 angle pdb=" C ARG D 532 " pdb=" N ASP D 533 " pdb=" CA ASP D 533 " ideal model delta sigma weight residual 122.62 152.41 -29.79 1.63e+00 3.76e-01 3.34e+02 ... (remaining 89014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 21393 16.14 - 32.28: 1053 32.28 - 48.41: 189 48.41 - 64.55: 162 64.55 - 80.69: 18 Dihedral angle restraints: 22815 sinusoidal: 12735 harmonic: 10080 Sorted by residual: dihedral pdb=" CA GLY E 645 " pdb=" C GLY E 645 " pdb=" N SER E 646 " pdb=" CA SER E 646 " ideal model delta harmonic sigma weight residual 0.00 -43.09 43.09 0 5.00e+00 4.00e-02 7.43e+01 dihedral pdb=" CA GLY I 645 " pdb=" C GLY I 645 " pdb=" N SER I 646 " pdb=" CA SER I 646 " ideal model delta harmonic sigma weight residual 0.00 -43.07 43.07 0 5.00e+00 4.00e-02 7.42e+01 dihedral pdb=" CA GLY A 645 " pdb=" C GLY A 645 " pdb=" N SER A 646 " pdb=" CA SER A 646 " ideal model delta harmonic sigma weight residual 0.00 -43.06 43.06 0 5.00e+00 4.00e-02 7.42e+01 ... (remaining 22812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2036 0.075 - 0.150: 1175 0.150 - 0.226: 532 0.226 - 0.301: 127 0.301 - 0.376: 27 Chirality restraints: 3897 Sorted by residual: chirality pdb=" CA TYR G 501 " pdb=" N TYR G 501 " pdb=" C TYR G 501 " pdb=" CB TYR G 501 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA TYR I 501 " pdb=" N TYR I 501 " pdb=" C TYR I 501 " pdb=" CB TYR I 501 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA TYR F 501 " pdb=" N TYR F 501 " pdb=" C TYR F 501 " pdb=" CB TYR F 501 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 3894 not shown) Planarity restraints: 7119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 572 " 0.085 2.00e-02 2.50e+03 1.55e-01 2.42e+02 pdb=" N SER D 573 " -0.269 2.00e-02 2.50e+03 pdb=" CA SER D 573 " 0.077 2.00e-02 2.50e+03 pdb=" H SER D 573 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 572 " 0.085 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" N SER G 573 " -0.268 2.00e-02 2.50e+03 pdb=" CA SER G 573 " 0.077 2.00e-02 2.50e+03 pdb=" H SER G 573 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 572 " -0.085 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" N SER H 573 " 0.268 2.00e-02 2.50e+03 pdb=" CA SER H 573 " -0.077 2.00e-02 2.50e+03 pdb=" H SER H 573 " -0.106 2.00e-02 2.50e+03 ... (remaining 7116 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.86: 1429 1.86 - 2.55: 50911 2.55 - 3.23: 167218 3.23 - 3.92: 216017 3.92 - 4.60: 333344 Nonbonded interactions: 768919 Sorted by model distance: nonbonded pdb=" HH TYR I 362 " pdb=" HG1 THR I 367 " model vdw 1.178 2.100 nonbonded pdb=" HH TYR E 362 " pdb=" HG1 THR E 367 " model vdw 1.178 2.100 nonbonded pdb=" HH TYR F 362 " pdb=" HG1 THR F 367 " model vdw 1.178 2.100 nonbonded pdb=" HH TYR D 362 " pdb=" HG1 THR D 367 " model vdw 1.178 2.100 nonbonded pdb=" HH TYR A 362 " pdb=" HG1 THR A 367 " model vdw 1.179 2.100 ... (remaining 768914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set refine NCS operators NCS operators will be refined. 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: 2.010 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: 0.720 Extract box with map and model: 9.330 Check model and map are aligned: 0.740 Set scattering table: 0.470 Process input model: 149.810 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 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 : 0.025 0.159 24516 Z= 1.607 Angle : 2.309 29.822 33183 Z= 1.599 Chirality : 0.112 0.376 3897 Planarity : 0.022 0.145 4221 Dihedral : 11.096 80.688 9270 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.98 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 0.93 % 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: -0.14 (0.16), residues: 2970 helix: -0.06 (0.15), residues: 1071 sheet: -1.08 (0.49), residues: 99 loop : 0.07 (0.16), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP H 580 HIS 0.010 0.004 HIS H 425 PHE 0.052 0.011 PHE E 377 TYR 0.112 0.017 TYR E 420 ARG 0.015 0.003 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.477 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: 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: symmetry clash REVERT: A 351 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 355 LEU cc_start: 0.8380 (tp) cc_final: 0.8061 (tt) REVERT: A 383 ILE cc_start: 0.6088 (mt) cc_final: 0.5847 (mm) REVERT: A 475 LYS cc_start: 0.7269 (mtmt) cc_final: 0.6961 (mttp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.4268 time to fit residues: 57.7197 Evaluate side-chains 75 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.7980 chunk 225 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 151 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 369 GLN A 522 GLN A 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24516 Z= 0.285 Angle : 0.875 16.065 33183 Z= 0.514 Chirality : 0.048 0.194 3897 Planarity : 0.021 0.425 4221 Dihedral : 9.437 113.943 3249 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.24 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -1.53 (0.15), residues: 2970 helix: -1.15 (0.13), residues: 1215 sheet: -2.84 (0.33), residues: 90 loop : -0.71 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 375 HIS 0.009 0.004 HIS F 425 PHE 0.022 0.002 PHE B 673 TYR 0.020 0.003 TYR F 444 ARG 0.010 0.001 ARG B 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.466 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 405 TYR cc_start: 0.7335 (p90) cc_final: 0.7114 (p90) REVERT: A 553 ILE cc_start: 0.8691 (mt) cc_final: 0.8310 (mt) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3666 time to fit residues: 44.1016 Evaluate side-chains 64 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 270 optimal weight: 0.6980 chunk 291 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 661 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24516 Z= 0.316 Angle : 0.771 15.315 33183 Z= 0.458 Chirality : 0.044 0.134 3897 Planarity : 0.018 0.364 4221 Dihedral : 9.905 129.446 3249 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.33 % Allowed : 2.29 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.24 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -1.85 (0.15), residues: 2970 helix: -1.26 (0.13), residues: 1197 sheet: -2.45 (0.39), residues: 90 loop : -1.07 (0.16), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 375 HIS 0.004 0.002 HIS F 425 PHE 0.015 0.002 PHE B 378 TYR 0.020 0.003 TYR E 444 ARG 0.016 0.001 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.434 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: A 385 LEU cc_start: 0.8716 (tp) cc_final: 0.8467 (tp) REVERT: A 400 ILE cc_start: 0.8084 (pt) cc_final: 0.7757 (pt) REVERT: A 532 ARG cc_start: 0.5183 (tpt170) cc_final: 0.4536 (tpt170) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.3416 time to fit residues: 32.7236 Evaluate side-chains 65 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 287 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 256 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 509 GLN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.7357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24516 Z= 0.299 Angle : 0.752 15.433 33183 Z= 0.440 Chirality : 0.044 0.152 3897 Planarity : 0.008 0.118 4221 Dihedral : 11.084 165.998 3249 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.24 % 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: -1.76 (0.15), residues: 2970 helix: -1.05 (0.14), residues: 1116 sheet: -3.29 (0.26), residues: 189 loop : -0.89 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP G 375 HIS 0.003 0.001 HIS A 425 PHE 0.014 0.002 PHE A 484 TYR 0.026 0.003 TYR A 557 ARG 0.012 0.001 ARG F 532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.399 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 SER cc_start: 0.9065 (t) cc_final: 0.8789 (m) REVERT: A 520 ILE cc_start: 0.9271 (mt) cc_final: 0.9039 (mt) REVERT: A 532 ARG cc_start: 0.5186 (tpt170) cc_final: 0.4651 (tpt170) REVERT: A 553 ILE cc_start: 0.8705 (mt) cc_final: 0.8342 (mt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2930 time to fit residues: 29.6832 Evaluate side-chains 62 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 0.0000 chunk 162 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 257 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.7958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 24516 Z= 0.240 Angle : 0.714 15.476 33183 Z= 0.416 Chirality : 0.044 0.152 3897 Planarity : 0.006 0.076 4221 Dihedral : 11.413 176.449 3249 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.24 % 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: -1.95 (0.15), residues: 2970 helix: -1.13 (0.14), residues: 1152 sheet: -3.35 (0.24), residues: 207 loop : -1.04 (0.17), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 375 HIS 0.005 0.002 HIS D 565 PHE 0.011 0.002 PHE C 378 TYR 0.019 0.002 TYR I 602 ARG 0.007 0.001 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.410 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.9330 (mt) cc_final: 0.8904 (tt) REVERT: A 484 PHE cc_start: 0.7672 (m-80) cc_final: 0.7410 (m-10) REVERT: A 520 ILE cc_start: 0.9270 (mt) cc_final: 0.9058 (mt) REVERT: A 532 ARG cc_start: 0.5131 (tpt170) cc_final: 0.4530 (tpt170) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2886 time to fit residues: 28.3128 Evaluate side-chains 63 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 0.0470 chunk 287 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 0.0570 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.8482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24516 Z= 0.190 Angle : 0.667 15.450 33183 Z= 0.385 Chirality : 0.044 0.147 3897 Planarity : 0.009 0.152 4221 Dihedral : 10.632 162.480 3249 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.24 % 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: -1.79 (0.15), residues: 2970 helix: -0.81 (0.14), residues: 1143 sheet: -1.94 (0.32), residues: 270 loop : -1.27 (0.17), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 375 HIS 0.003 0.001 HIS D 425 PHE 0.015 0.002 PHE B 471 TYR 0.024 0.002 TYR I 557 ARG 0.018 0.001 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.462 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 TYR cc_start: 0.7714 (p90) cc_final: 0.7465 (p90) REVERT: A 472 LEU cc_start: 0.9309 (mt) cc_final: 0.8929 (tt) REVERT: A 484 PHE cc_start: 0.7539 (m-80) cc_final: 0.7194 (m-10) REVERT: A 520 ILE cc_start: 0.9276 (mt) cc_final: 0.9058 (mt) REVERT: A 532 ARG cc_start: 0.5212 (tpt170) cc_final: 0.4573 (tpt170) REVERT: A 553 ILE cc_start: 0.8849 (mt) cc_final: 0.8596 (mp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3057 time to fit residues: 30.9385 Evaluate side-chains 66 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 286 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.9221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 24516 Z= 0.441 Angle : 0.844 15.162 33183 Z= 0.492 Chirality : 0.047 0.153 3897 Planarity : 0.007 0.062 4221 Dihedral : 11.330 173.793 3249 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 30.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 0.33 % Allowed : 3.27 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.14), residues: 2970 helix: -1.57 (0.12), residues: 1152 sheet: -2.06 (0.29), residues: 270 loop : -1.74 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 375 HIS 0.006 0.002 HIS E 565 PHE 0.025 0.003 PHE A 378 TYR 0.021 0.003 TYR A 420 ARG 0.004 0.001 ARG F 569 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.433 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.7479 (m-80) cc_final: 0.7247 (m-80) REVERT: A 520 ILE cc_start: 0.9267 (mt) cc_final: 0.9060 (mt) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.2407 time to fit residues: 22.0818 Evaluate side-chains 61 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 195 optimal weight: 0.4980 chunk 141 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 225 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.9543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24516 Z= 0.192 Angle : 0.682 15.760 33183 Z= 0.398 Chirality : 0.046 0.164 3897 Planarity : 0.006 0.061 4221 Dihedral : 11.253 175.890 3249 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 2970 helix: -0.97 (0.14), residues: 1143 sheet: -1.76 (0.32), residues: 270 loop : -1.65 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 375 HIS 0.003 0.001 HIS B 425 PHE 0.027 0.002 PHE D 673 TYR 0.030 0.003 TYR B 557 ARG 0.009 0.001 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.437 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.9324 (mt) cc_final: 0.8950 (tt) REVERT: A 520 ILE cc_start: 0.9255 (mt) cc_final: 0.8910 (tt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2631 time to fit residues: 25.2676 Evaluate side-chains 68 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 3.9990 chunk 274 optimal weight: 10.0000 chunk 250 optimal weight: 0.5980 chunk 266 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 252 optimal weight: 1.9990 chunk 265 optimal weight: 0.3980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.9814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24516 Z= 0.222 Angle : 0.666 15.598 33183 Z= 0.386 Chirality : 0.044 0.159 3897 Planarity : 0.005 0.053 4221 Dihedral : 11.249 177.073 3249 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.15), residues: 2970 helix: -0.85 (0.14), residues: 1143 sheet: -1.44 (0.38), residues: 216 loop : -1.78 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 375 HIS 0.013 0.003 HIS D 565 PHE 0.024 0.002 PHE C 673 TYR 0.020 0.002 TYR F 557 ARG 0.005 0.001 ARG D 491 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.446 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.8515 (tp) cc_final: 0.8309 (tp) REVERT: A 472 LEU cc_start: 0.9316 (mt) cc_final: 0.8940 (tt) REVERT: A 520 ILE cc_start: 0.9245 (mt) cc_final: 0.9021 (mt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2622 time to fit residues: 23.7684 Evaluate side-chains 65 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 295 optimal weight: 5.9990 chunk 272 optimal weight: 0.7980 chunk 235 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 181 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 1.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24516 Z= 0.185 Angle : 0.643 15.446 33183 Z= 0.374 Chirality : 0.044 0.139 3897 Planarity : 0.007 0.110 4221 Dihedral : 11.139 176.747 3249 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.24 % 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: -1.92 (0.15), residues: 2970 helix: -0.56 (0.15), residues: 1152 sheet: -1.50 (0.38), residues: 216 loop : -1.79 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 375 HIS 0.002 0.001 HIS B 425 PHE 0.023 0.002 PHE H 673 TYR 0.020 0.003 TYR E 638 ARG 0.013 0.001 ARG A 637 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.454 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 LEU cc_start: 0.7844 (tp) cc_final: 0.7368 (tt) REVERT: A 356 ASN cc_start: 0.8331 (m-40) cc_final: 0.8001 (m-40) REVERT: A 385 LEU cc_start: 0.8555 (tp) cc_final: 0.8338 (tp) REVERT: A 472 LEU cc_start: 0.9313 (mt) cc_final: 0.8961 (tt) REVERT: A 520 ILE cc_start: 0.9220 (mt) cc_final: 0.8922 (tt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2891 time to fit residues: 25.7940 Evaluate side-chains 65 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 217 optimal weight: 0.3980 chunk 34 optimal weight: 0.0370 chunk 65 optimal weight: 0.6980 chunk 235 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.110334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.084214 restraints weight = 31511.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.088621 restraints weight = 16837.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.091560 restraints weight = 10957.443| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 1.0100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24516 Z= 0.167 Angle : 0.624 15.430 33183 Z= 0.358 Chirality : 0.044 0.141 3897 Planarity : 0.006 0.059 4221 Dihedral : 10.979 175.917 3249 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.24 % 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: -1.97 (0.15), residues: 2970 helix: -0.43 (0.15), residues: 1206 sheet: -1.51 (0.37), residues: 216 loop : -2.02 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 375 HIS 0.002 0.001 HIS B 425 PHE 0.021 0.002 PHE H 673 TYR 0.019 0.002 TYR H 570 ARG 0.011 0.001 ARG F 637 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4760.65 seconds wall clock time: 88 minutes 0.68 seconds (5280.68 seconds total)