Starting phenix.real_space_refine (version: dev) on Thu Dec 22 09:17:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/12_2022/7k08_22589.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/12_2022/7k08_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_22589/12_2022/7k08_22589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/12_2022/7k08_22589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/12_2022/7k08_22589.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k08_22589/12_2022/7k08_22589.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Convert atoms to be neutral 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 20.72, per 1000 atoms: 0.43 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: 42.24 Conformation dependent library (CDL) restraints added in 3.7 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: 1.45 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: 18.45 Time building geometry restraints manager: 43.67 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: 18603 16.14 - 32.28: 900 32.28 - 48.41: 90 48.41 - 64.55: 63 64.55 - 80.69: 18 Dihedral angle restraints: 19674 sinusoidal: 9594 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 19671 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. 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. 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: 4.300 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: 1.530 Extract box with map and model: 9.760 Check model and map are aligned: 0.680 Convert atoms to be neutral: 0.400 Process input model: 146.220 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 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 : 2.305 29.822 33183 Z= 1.596 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 : 6.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.98 % Favored : 94.85 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.442 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 outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3741 time to fit residues: 51.8943 Evaluate side-chains 74 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5581 ------------------------------------------------------------------------------- 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: 0.5980 chunk 225 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 232 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 173 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 391 ASN A 522 GLN A 588 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 24516 Z= 0.297 Angle : 0.887 15.943 33183 Z= 0.507 Chirality : 0.048 0.204 3897 Planarity : 0.020 0.407 4221 Dihedral : 9.605 119.682 3249 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.00 % 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: -1.58 (0.15), residues: 2970 helix: -1.13 (0.13), residues: 1206 sheet: -2.96 (0.31), residues: 90 loop : -0.78 (0.16), residues: 1674 *********************** 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 103 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.518 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 outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3048 time to fit residues: 37.1500 Evaluate side-chains 69 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5685 ------------------------------------------------------------------------------- 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: 1.9990 chunk 224 optimal weight: 8.9990 chunk 183 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 240 optimal weight: 0.0570 chunk 267 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 509 GLN I 661 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 24516 Z= 0.266 Angle : 0.787 16.602 33183 Z= 0.453 Chirality : 0.045 0.139 3897 Planarity : 0.012 0.228 4221 Dihedral : 7.150 33.879 3249 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 0.00 % 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: -1.90 (0.15), residues: 2970 helix: -1.27 (0.13), residues: 1197 sheet: -2.96 (0.39), residues: 99 loop : -1.07 (0.16), residues: 1674 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3148 time to fit residues: 31.1836 Evaluate side-chains 64 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5559 ------------------------------------------------------------------------------- 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: 1.9990 chunk 203 optimal weight: 7.9990 chunk 140 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 0.4980 chunk 287 optimal weight: 4.9990 chunk 141 optimal weight: 0.0050 chunk 256 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 24516 Z= 0.195 Angle : 0.699 15.888 33183 Z= 0.397 Chirality : 0.043 0.154 3897 Planarity : 0.006 0.065 4221 Dihedral : 6.575 28.503 3249 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer Outliers : 0.00 % 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: -2.00 (0.15), residues: 2970 helix: -1.08 (0.14), residues: 1179 sheet: -3.13 (0.35), residues: 144 loop : -1.30 (0.16), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 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 outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2706 time to fit residues: 27.5863 Evaluate side-chains 64 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6403 ------------------------------------------------------------------------------- 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: 0.0170 chunk 162 optimal weight: 0.9980 chunk 4 optimal weight: 0.0370 chunk 213 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 661 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.7682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 24516 Z= 0.212 Angle : 0.702 15.977 33183 Z= 0.397 Chirality : 0.045 0.151 3897 Planarity : 0.006 0.077 4221 Dihedral : 6.514 26.944 3249 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer Outliers : 0.00 % 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: -2.07 (0.15), residues: 2970 helix: -0.92 (0.15), residues: 1125 sheet: -2.04 (0.31), residues: 270 loop : -1.54 (0.16), residues: 1575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.440 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 outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2566 time to fit residues: 25.0873 Evaluate side-chains 58 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5569 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 chunk 287 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6146 moved from start: 0.8135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 24516 Z= 0.266 Angle : 0.708 15.689 33183 Z= 0.403 Chirality : 0.044 0.175 3897 Planarity : 0.005 0.046 4221 Dihedral : 6.304 22.274 3249 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer Outliers : 0.00 % 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: -2.17 (0.15), residues: 2970 helix: -1.14 (0.14), residues: 1125 sheet: -2.02 (0.29), residues: 252 loop : -1.53 (0.16), residues: 1593 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.448 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 outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2086 time to fit residues: 19.1124 Evaluate side-chains 62 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5726 ------------------------------------------------------------------------------- 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: 4.9990 chunk 163 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 162 optimal weight: 0.4980 chunk 241 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.8808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 24516 Z= 0.299 Angle : 0.741 15.131 33183 Z= 0.413 Chirality : 0.045 0.148 3897 Planarity : 0.007 0.094 4221 Dihedral : 6.378 21.756 3249 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer Outliers : 0.00 % 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: -2.42 (0.15), residues: 2970 helix: -1.30 (0.14), residues: 1152 sheet: -2.25 (0.31), residues: 270 loop : -1.68 (0.16), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.447 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 outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2148 time to fit residues: 19.7818 Evaluate side-chains 61 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6095 ------------------------------------------------------------------------------- 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: 0.0980 chunk 114 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 225 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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: 0.6240 moved from start: 0.9200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 24516 Z= 0.247 Angle : 0.680 15.747 33183 Z= 0.383 Chirality : 0.043 0.140 3897 Planarity : 0.005 0.044 4221 Dihedral : 6.212 21.264 3249 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer Outliers : 0.00 % 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: -2.38 (0.15), residues: 2970 helix: -1.09 (0.14), residues: 1152 sheet: -2.12 (0.31), residues: 270 loop : -1.85 (0.16), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.517 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 outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2508 time to fit residues: 20.9340 Evaluate side-chains 62 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5787 ------------------------------------------------------------------------------- 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: 0.0070 chunk 250 optimal weight: 0.4980 chunk 266 optimal weight: 0.3980 chunk 160 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 81 optimal weight: 0.0010 chunk 241 optimal weight: 0.0270 chunk 252 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 overall best weight: 0.1862 ------------------------------------------------------------------------------- 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: 0.6118 moved from start: 0.9487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 24516 Z= 0.175 Angle : 0.651 15.476 33183 Z= 0.356 Chirality : 0.045 0.149 3897 Planarity : 0.005 0.038 4221 Dihedral : 5.969 20.597 3249 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer Outliers : 0.00 % 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: -2.36 (0.15), residues: 2970 helix: -0.92 (0.14), residues: 1206 sheet: -1.80 (0.37), residues: 216 loop : -2.07 (0.16), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.455 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 outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2143 time to fit residues: 18.7929 Evaluate side-chains 62 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6168 ------------------------------------------------------------------------------- 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: 6.9990 chunk 282 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 196 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 144 optimal weight: 0.0570 overall best weight: 1.2902 ------------------------------------------------------------------------------- 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: 0.6216 moved from start: 0.9718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 24516 Z= 0.231 Angle : 0.660 15.316 33183 Z= 0.372 Chirality : 0.044 0.145 3897 Planarity : 0.005 0.039 4221 Dihedral : 5.946 21.507 3249 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer Outliers : 0.33 % 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: -2.27 (0.15), residues: 2970 helix: -1.13 (0.14), residues: 1152 sheet: -1.77 (0.37), residues: 216 loop : -1.75 (0.16), residues: 1602 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.402 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 outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.2132 time to fit residues: 19.0506 Evaluate side-chains 61 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6376 ------------------------------------------------------------------------------- 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: 0.0570 chunk 250 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 98 optimal weight: 0.0570 chunk 242 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.109387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.083660 restraints weight = 31412.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.087970 restraints weight = 17693.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.090824 restraints weight = 11672.720| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.9862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 24516 Z= 0.173 Angle : 0.640 15.249 33183 Z= 0.353 Chirality : 0.044 0.132 3897 Planarity : 0.005 0.035 4221 Dihedral : 5.816 21.817 3249 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer Outliers : 0.00 % 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: -2.26 (0.15), residues: 2970 helix: -0.81 (0.14), residues: 1206 sheet: -1.82 (0.35), residues: 216 loop : -2.03 (0.15), residues: 1548 =============================================================================== Job complete usr+sys time: 4437.93 seconds wall clock time: 81 minutes 29.61 seconds (4889.61 seconds total)