Starting phenix.real_space_refine on Wed Mar 20 10:11:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/03_2024/6okt_20104.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/03_2024/6okt_20104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/03_2024/6okt_20104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/03_2024/6okt_20104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/03_2024/6okt_20104.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/03_2024/6okt_20104.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 16926 2.51 5 N 4368 2.21 5 O 5712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 232": "NH1" <-> "NH2" Residue "H ASP 282": "OD1" <-> "OD2" Residue "H ARG 290": "NH1" <-> "NH2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H ASP 369": "OD1" <-> "OD2" Residue "H TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 520": "OD1" <-> "OD2" Residue "H TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 537": "OD1" <-> "OD2" Residue "H PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 568": "OD1" <-> "OD2" Residue "H ARG 607": "NH1" <-> "NH2" Residue "H TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I ASP 282": "OD1" <-> "OD2" Residue "I ARG 290": "NH1" <-> "NH2" Residue "I ARG 325": "NH1" <-> "NH2" Residue "I ASP 369": "OD1" <-> "OD2" Residue "I TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 520": "OD1" <-> "OD2" Residue "I TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 537": "OD1" <-> "OD2" Residue "I PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 568": "OD1" <-> "OD2" Residue "I ARG 607": "NH1" <-> "NH2" Residue "I TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J ASP 282": "OD1" <-> "OD2" Residue "J ARG 290": "NH1" <-> "NH2" Residue "J ARG 325": "NH1" <-> "NH2" Residue "J ASP 369": "OD1" <-> "OD2" Residue "J TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 520": "OD1" <-> "OD2" Residue "J TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 537": "OD1" <-> "OD2" Residue "J PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 568": "OD1" <-> "OD2" Residue "J ARG 607": "NH1" <-> "NH2" Residue "J TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K ASP 282": "OD1" <-> "OD2" Residue "K ARG 290": "NH1" <-> "NH2" Residue "K ARG 325": "NH1" <-> "NH2" Residue "K ASP 369": "OD1" <-> "OD2" Residue "K TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 520": "OD1" <-> "OD2" Residue "K TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 537": "OD1" <-> "OD2" Residue "K PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 568": "OD1" <-> "OD2" Residue "K ARG 607": "NH1" <-> "NH2" Residue "K TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L ASP 282": "OD1" <-> "OD2" Residue "L ARG 290": "NH1" <-> "NH2" Residue "L ARG 325": "NH1" <-> "NH2" Residue "L ASP 369": "OD1" <-> "OD2" Residue "L TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 520": "OD1" <-> "OD2" Residue "L TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 537": "OD1" <-> "OD2" Residue "L PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 568": "OD1" <-> "OD2" Residue "L ARG 607": "NH1" <-> "NH2" Residue "L TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ASP 282": "OD1" <-> "OD2" Residue "M ARG 290": "NH1" <-> "NH2" Residue "M ARG 325": "NH1" <-> "NH2" Residue "M ASP 369": "OD1" <-> "OD2" Residue "M TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 520": "OD1" <-> "OD2" Residue "M TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 537": "OD1" <-> "OD2" Residue "M PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 568": "OD1" <-> "OD2" Residue "M ARG 607": "NH1" <-> "NH2" Residue "M TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 232": "NH1" <-> "NH2" Residue "N ASP 282": "OD1" <-> "OD2" Residue "N ARG 290": "NH1" <-> "NH2" Residue "N ARG 325": "NH1" <-> "NH2" Residue "N ASP 369": "OD1" <-> "OD2" Residue "N TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 520": "OD1" <-> "OD2" Residue "N TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 537": "OD1" <-> "OD2" Residue "N PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 568": "OD1" <-> "OD2" Residue "N ARG 607": "NH1" <-> "NH2" Residue "N TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27048 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "I" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "J" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "K" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "L" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "M" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "N" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Time building chain proxies: 14.50, per 1000 atoms: 0.54 Number of scatterers: 27048 At special positions: 0 Unit cell: (181.25, 179.8, 134.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 5712 8.00 N 4368 7.00 C 16926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.00 Conformation dependent library (CDL) restraints added in 5.5 seconds 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6468 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 64 sheets defined 14.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'H' and resid 226 through 232 Processing helix chain 'H' and resid 272 through 278 removed outlier: 3.836A pdb=" N SER H 278 " --> pdb=" O TYR H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 290 Processing helix chain 'H' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE H 429 " --> pdb=" O GLU H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 472 Processing helix chain 'H' and resid 503 through 505 No H-bonds generated for 'chain 'H' and resid 503 through 505' Processing helix chain 'H' and resid 506 through 513 removed outlier: 4.144A pdb=" N ILE H 510 " --> pdb=" O TYR H 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE H 513 " --> pdb=" O GLN H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 546 through 555 removed outlier: 3.698A pdb=" N PHE H 555 " --> pdb=" O ILE H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 593 removed outlier: 4.037A pdb=" N LYS H 593 " --> pdb=" O LYS H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU H 662 " --> pdb=" O PRO H 659 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 232 Processing helix chain 'I' and resid 272 through 278 removed outlier: 3.835A pdb=" N SER I 278 " --> pdb=" O TYR I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 290 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE I 429 " --> pdb=" O GLU I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 472 Processing helix chain 'I' and resid 503 through 505 No H-bonds generated for 'chain 'I' and resid 503 through 505' Processing helix chain 'I' and resid 506 through 513 removed outlier: 4.144A pdb=" N ILE I 510 " --> pdb=" O TYR I 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE I 513 " --> pdb=" O GLN I 509 " (cutoff:3.500A) Processing helix chain 'I' and resid 546 through 555 removed outlier: 3.697A pdb=" N PHE I 555 " --> pdb=" O ILE I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 581 through 593 removed outlier: 4.037A pdb=" N LYS I 593 " --> pdb=" O LYS I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU I 662 " --> pdb=" O PRO I 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 232 Processing helix chain 'J' and resid 272 through 278 removed outlier: 3.835A pdb=" N SER J 278 " --> pdb=" O TYR J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 425 through 429 removed outlier: 3.712A pdb=" N ILE J 429 " --> pdb=" O GLU J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 463 through 472 Processing helix chain 'J' and resid 503 through 505 No H-bonds generated for 'chain 'J' and resid 503 through 505' Processing helix chain 'J' and resid 506 through 513 removed outlier: 4.143A pdb=" N ILE J 510 " --> pdb=" O TYR J 506 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE J 513 " --> pdb=" O GLN J 509 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 555 removed outlier: 3.698A pdb=" N PHE J 555 " --> pdb=" O ILE J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 593 removed outlier: 4.038A pdb=" N LYS J 593 " --> pdb=" O LYS J 589 " (cutoff:3.500A) Processing helix chain 'J' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU J 662 " --> pdb=" O PRO J 659 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 232 Processing helix chain 'K' and resid 272 through 278 removed outlier: 3.835A pdb=" N SER K 278 " --> pdb=" O TYR K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 290 Processing helix chain 'K' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE K 429 " --> pdb=" O GLU K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 472 Processing helix chain 'K' and resid 503 through 505 No H-bonds generated for 'chain 'K' and resid 503 through 505' Processing helix chain 'K' and resid 506 through 513 removed outlier: 4.144A pdb=" N ILE K 510 " --> pdb=" O TYR K 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE K 513 " --> pdb=" O GLN K 509 " (cutoff:3.500A) Processing helix chain 'K' and resid 546 through 555 removed outlier: 3.698A pdb=" N PHE K 555 " --> pdb=" O ILE K 551 " (cutoff:3.500A) Processing helix chain 'K' and resid 581 through 593 removed outlier: 4.038A pdb=" N LYS K 593 " --> pdb=" O LYS K 589 " (cutoff:3.500A) Processing helix chain 'K' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU K 662 " --> pdb=" O PRO K 659 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 232 Processing helix chain 'L' and resid 272 through 278 removed outlier: 3.836A pdb=" N SER L 278 " --> pdb=" O TYR L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 290 Processing helix chain 'L' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE L 429 " --> pdb=" O GLU L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 472 Processing helix chain 'L' and resid 503 through 505 No H-bonds generated for 'chain 'L' and resid 503 through 505' Processing helix chain 'L' and resid 506 through 513 removed outlier: 4.144A pdb=" N ILE L 510 " --> pdb=" O TYR L 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 513 " --> pdb=" O GLN L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 546 through 555 removed outlier: 3.699A pdb=" N PHE L 555 " --> pdb=" O ILE L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 581 through 593 removed outlier: 4.038A pdb=" N LYS L 593 " --> pdb=" O LYS L 589 " (cutoff:3.500A) Processing helix chain 'L' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU L 662 " --> pdb=" O PRO L 659 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 232 Processing helix chain 'M' and resid 272 through 278 removed outlier: 3.836A pdb=" N SER M 278 " --> pdb=" O TYR M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 290 Processing helix chain 'M' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE M 429 " --> pdb=" O GLU M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 463 through 472 Processing helix chain 'M' and resid 503 through 505 No H-bonds generated for 'chain 'M' and resid 503 through 505' Processing helix chain 'M' and resid 506 through 513 removed outlier: 4.144A pdb=" N ILE M 510 " --> pdb=" O TYR M 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE M 513 " --> pdb=" O GLN M 509 " (cutoff:3.500A) Processing helix chain 'M' and resid 546 through 555 removed outlier: 3.698A pdb=" N PHE M 555 " --> pdb=" O ILE M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 581 through 593 removed outlier: 4.038A pdb=" N LYS M 593 " --> pdb=" O LYS M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU M 662 " --> pdb=" O PRO M 659 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 232 Processing helix chain 'N' and resid 272 through 278 removed outlier: 3.835A pdb=" N SER N 278 " --> pdb=" O TYR N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 290 Processing helix chain 'N' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE N 429 " --> pdb=" O GLU N 426 " (cutoff:3.500A) Processing helix chain 'N' and resid 463 through 472 Processing helix chain 'N' and resid 503 through 505 No H-bonds generated for 'chain 'N' and resid 503 through 505' Processing helix chain 'N' and resid 506 through 513 removed outlier: 4.143A pdb=" N ILE N 510 " --> pdb=" O TYR N 506 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE N 513 " --> pdb=" O GLN N 509 " (cutoff:3.500A) Processing helix chain 'N' and resid 546 through 555 removed outlier: 3.699A pdb=" N PHE N 555 " --> pdb=" O ILE N 551 " (cutoff:3.500A) Processing helix chain 'N' and resid 581 through 593 removed outlier: 4.038A pdb=" N LYS N 593 " --> pdb=" O LYS N 589 " (cutoff:3.500A) Processing helix chain 'N' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU N 662 " --> pdb=" O PRO N 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 236 through 238 Processing sheet with id=AA2, first strand: chain 'H' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL H 300 " --> pdb=" O THR H 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR H 398 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 302 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR H 396 " --> pdb=" O VAL H 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET H 304 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG H 394 " --> pdb=" O MET H 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS H 306 " --> pdb=" O ASN H 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL H 300 " --> pdb=" O THR H 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR H 398 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 302 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR H 396 " --> pdb=" O VAL H 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET H 304 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG H 394 " --> pdb=" O MET H 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS H 306 " --> pdb=" O ASN H 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 314 through 326 removed outlier: 3.687A pdb=" N ASN H 371 " --> pdb=" O ARG N 325 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS N 321 " --> pdb=" O TRP H 375 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN N 371 " --> pdb=" O ARG M 325 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG M 325 " --> pdb=" O ASN N 371 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL M 323 " --> pdb=" O GLU N 373 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS M 321 " --> pdb=" O TRP N 375 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN M 371 " --> pdb=" O ARG L 325 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS L 321 " --> pdb=" O TRP M 375 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE M 381 " --> pdb=" O ALA L 315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 315 " --> pdb=" O ILE M 381 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE L 381 " --> pdb=" O ALA K 315 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 315 " --> pdb=" O ILE L 381 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN K 371 " --> pdb=" O ARG J 325 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS J 321 " --> pdb=" O TRP K 375 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN J 371 " --> pdb=" O ARG I 325 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS I 321 " --> pdb=" O TRP J 375 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN I 371 " --> pdb=" O ARG H 325 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS H 321 " --> pdb=" O TRP I 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 420 through 423 removed outlier: 3.813A pdb=" N SER H 420 " --> pdb=" O LEU H 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL H 406 " --> pdb=" O SER H 484 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER H 484 " --> pdb=" O VAL H 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN H 482 " --> pdb=" O PRO H 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR H 410 " --> pdb=" O THR H 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR H 480 " --> pdb=" O THR H 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 489 through 490 removed outlier: 3.856A pdb=" N THR H 489 " --> pdb=" O VAL H 497 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 525 through 531 Processing sheet with id=AA8, first strand: chain 'H' and resid 558 through 560 removed outlier: 3.604A pdb=" N LEU H 564 " --> pdb=" O ILE H 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 618 through 619 Processing sheet with id=AB1, first strand: chain 'H' and resid 651 through 658 removed outlier: 3.745A pdb=" N THR H 680 " --> pdb=" O SER H 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 236 through 238 Processing sheet with id=AB3, first strand: chain 'I' and resid 299 through 311 removed outlier: 5.322A pdb=" N VAL I 300 " --> pdb=" O THR I 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR I 398 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL I 302 " --> pdb=" O TYR I 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR I 396 " --> pdb=" O VAL I 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET I 304 " --> pdb=" O ARG I 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG I 394 " --> pdb=" O MET I 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS I 306 " --> pdb=" O ASN I 392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 299 through 311 removed outlier: 5.322A pdb=" N VAL I 300 " --> pdb=" O THR I 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR I 398 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL I 302 " --> pdb=" O TYR I 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR I 396 " --> pdb=" O VAL I 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET I 304 " --> pdb=" O ARG I 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG I 394 " --> pdb=" O MET I 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS I 306 " --> pdb=" O ASN I 392 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER I 420 " --> pdb=" O LEU I 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL I 406 " --> pdb=" O SER I 484 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER I 484 " --> pdb=" O VAL I 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN I 482 " --> pdb=" O PRO I 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR I 410 " --> pdb=" O THR I 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR I 480 " --> pdb=" O THR I 410 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 489 through 490 removed outlier: 3.855A pdb=" N THR I 489 " --> pdb=" O VAL I 497 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 525 through 531 Processing sheet with id=AB8, first strand: chain 'I' and resid 558 through 560 removed outlier: 3.603A pdb=" N LEU I 564 " --> pdb=" O ILE I 571 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 618 through 619 Processing sheet with id=AC1, first strand: chain 'I' and resid 651 through 658 removed outlier: 3.744A pdb=" N THR I 680 " --> pdb=" O SER I 728 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 236 through 238 Processing sheet with id=AC3, first strand: chain 'J' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL J 300 " --> pdb=" O THR J 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR J 398 " --> pdb=" O VAL J 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL J 302 " --> pdb=" O TYR J 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR J 396 " --> pdb=" O VAL J 302 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS J 306 " --> pdb=" O ASN J 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL J 300 " --> pdb=" O THR J 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR J 398 " --> pdb=" O VAL J 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL J 302 " --> pdb=" O TYR J 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR J 396 " --> pdb=" O VAL J 302 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS J 306 " --> pdb=" O ASN J 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER J 420 " --> pdb=" O LEU J 412 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL J 406 " --> pdb=" O SER J 484 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER J 484 " --> pdb=" O VAL J 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN J 482 " --> pdb=" O PRO J 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR J 410 " --> pdb=" O THR J 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR J 480 " --> pdb=" O THR J 410 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 489 through 490 removed outlier: 3.855A pdb=" N THR J 489 " --> pdb=" O VAL J 497 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 525 through 531 Processing sheet with id=AC8, first strand: chain 'J' and resid 558 through 560 removed outlier: 3.602A pdb=" N LEU J 564 " --> pdb=" O ILE J 571 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 618 through 619 Processing sheet with id=AD1, first strand: chain 'J' and resid 651 through 658 removed outlier: 3.745A pdb=" N THR J 680 " --> pdb=" O SER J 728 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 236 through 238 Processing sheet with id=AD3, first strand: chain 'K' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL K 300 " --> pdb=" O THR K 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR K 398 " --> pdb=" O VAL K 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL K 302 " --> pdb=" O TYR K 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR K 396 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N MET K 304 " --> pdb=" O ARG K 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG K 394 " --> pdb=" O MET K 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS K 306 " --> pdb=" O ASN K 392 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL K 300 " --> pdb=" O THR K 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR K 398 " --> pdb=" O VAL K 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL K 302 " --> pdb=" O TYR K 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR K 396 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N MET K 304 " --> pdb=" O ARG K 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG K 394 " --> pdb=" O MET K 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS K 306 " --> pdb=" O ASN K 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER K 420 " --> pdb=" O LEU K 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL K 406 " --> pdb=" O SER K 484 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER K 484 " --> pdb=" O VAL K 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN K 482 " --> pdb=" O PRO K 408 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR K 410 " --> pdb=" O THR K 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR K 480 " --> pdb=" O THR K 410 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 489 through 490 removed outlier: 3.855A pdb=" N THR K 489 " --> pdb=" O VAL K 497 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 525 through 531 Processing sheet with id=AD8, first strand: chain 'K' and resid 558 through 560 removed outlier: 3.603A pdb=" N LEU K 564 " --> pdb=" O ILE K 571 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 618 through 619 Processing sheet with id=AE1, first strand: chain 'K' and resid 651 through 658 removed outlier: 3.745A pdb=" N THR K 680 " --> pdb=" O SER K 728 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 236 through 238 Processing sheet with id=AE3, first strand: chain 'L' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL L 300 " --> pdb=" O THR L 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR L 398 " --> pdb=" O VAL L 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL L 302 " --> pdb=" O TYR L 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR L 396 " --> pdb=" O VAL L 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET L 304 " --> pdb=" O ARG L 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG L 394 " --> pdb=" O MET L 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 306 " --> pdb=" O ASN L 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL L 300 " --> pdb=" O THR L 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR L 398 " --> pdb=" O VAL L 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL L 302 " --> pdb=" O TYR L 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR L 396 " --> pdb=" O VAL L 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET L 304 " --> pdb=" O ARG L 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG L 394 " --> pdb=" O MET L 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 306 " --> pdb=" O ASN L 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER L 420 " --> pdb=" O LEU L 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL L 406 " --> pdb=" O SER L 484 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER L 484 " --> pdb=" O VAL L 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN L 482 " --> pdb=" O PRO L 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR L 410 " --> pdb=" O THR L 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR L 480 " --> pdb=" O THR L 410 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 489 through 490 removed outlier: 3.856A pdb=" N THR L 489 " --> pdb=" O VAL L 497 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 525 through 531 Processing sheet with id=AE8, first strand: chain 'L' and resid 558 through 560 removed outlier: 3.603A pdb=" N LEU L 564 " --> pdb=" O ILE L 571 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 618 through 619 Processing sheet with id=AF1, first strand: chain 'L' and resid 651 through 658 removed outlier: 3.744A pdb=" N THR L 680 " --> pdb=" O SER L 728 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 236 through 238 Processing sheet with id=AF3, first strand: chain 'M' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL M 300 " --> pdb=" O THR M 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR M 398 " --> pdb=" O VAL M 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL M 302 " --> pdb=" O TYR M 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR M 396 " --> pdb=" O VAL M 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET M 304 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG M 394 " --> pdb=" O MET M 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS M 306 " --> pdb=" O ASN M 392 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL M 300 " --> pdb=" O THR M 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR M 398 " --> pdb=" O VAL M 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL M 302 " --> pdb=" O TYR M 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR M 396 " --> pdb=" O VAL M 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET M 304 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG M 394 " --> pdb=" O MET M 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS M 306 " --> pdb=" O ASN M 392 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER M 420 " --> pdb=" O LEU M 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL M 406 " --> pdb=" O SER M 484 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER M 484 " --> pdb=" O VAL M 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN M 482 " --> pdb=" O PRO M 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR M 410 " --> pdb=" O THR M 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR M 480 " --> pdb=" O THR M 410 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 489 through 490 removed outlier: 3.855A pdb=" N THR M 489 " --> pdb=" O VAL M 497 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 525 through 531 Processing sheet with id=AF8, first strand: chain 'M' and resid 558 through 560 removed outlier: 3.604A pdb=" N LEU M 564 " --> pdb=" O ILE M 571 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 618 through 619 Processing sheet with id=AG1, first strand: chain 'M' and resid 651 through 658 removed outlier: 3.744A pdb=" N THR M 680 " --> pdb=" O SER M 728 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 236 through 238 Processing sheet with id=AG3, first strand: chain 'N' and resid 299 through 311 removed outlier: 5.322A pdb=" N VAL N 300 " --> pdb=" O THR N 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR N 398 " --> pdb=" O VAL N 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL N 302 " --> pdb=" O TYR N 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR N 396 " --> pdb=" O VAL N 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET N 304 " --> pdb=" O ARG N 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG N 394 " --> pdb=" O MET N 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS N 306 " --> pdb=" O ASN N 392 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 299 through 311 removed outlier: 5.322A pdb=" N VAL N 300 " --> pdb=" O THR N 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR N 398 " --> pdb=" O VAL N 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL N 302 " --> pdb=" O TYR N 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR N 396 " --> pdb=" O VAL N 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET N 304 " --> pdb=" O ARG N 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG N 394 " --> pdb=" O MET N 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS N 306 " --> pdb=" O ASN N 392 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER N 420 " --> pdb=" O LEU N 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL N 406 " --> pdb=" O SER N 484 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER N 484 " --> pdb=" O VAL N 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN N 482 " --> pdb=" O PRO N 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR N 410 " --> pdb=" O THR N 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR N 480 " --> pdb=" O THR N 410 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 489 through 490 removed outlier: 3.855A pdb=" N THR N 489 " --> pdb=" O VAL N 497 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 525 through 531 Processing sheet with id=AG8, first strand: chain 'N' and resid 558 through 560 removed outlier: 3.603A pdb=" N LEU N 564 " --> pdb=" O ILE N 571 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 618 through 619 Processing sheet with id=AH1, first strand: chain 'N' and resid 651 through 658 removed outlier: 3.744A pdb=" N THR N 680 " --> pdb=" O SER N 728 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2256 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: 9.54 Time building geometry restraints manager: 11.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8597 1.34 - 1.45: 3789 1.45 - 1.57: 15054 1.57 - 1.68: 0 1.68 - 1.80: 77 Bond restraints: 27517 Sorted by residual: bond pdb=" C LYS H 541 " pdb=" N THR H 542 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.47e+00 bond pdb=" C LYS L 541 " pdb=" N THR L 542 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.46e+00 bond pdb=" C LYS K 541 " pdb=" N THR K 542 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.43e+00 bond pdb=" C LYS N 541 " pdb=" N THR N 542 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.41e+00 bond pdb=" C LYS I 541 " pdb=" N THR I 542 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.37e+00 ... (remaining 27512 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.07: 554 106.07 - 113.06: 14870 113.06 - 120.04: 9571 120.04 - 127.02: 12107 127.02 - 134.01: 215 Bond angle restraints: 37317 Sorted by residual: angle pdb=" C ARG L 232 " pdb=" N ASN L 233 " pdb=" CA ASN L 233 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.79e+01 angle pdb=" C ARG N 232 " pdb=" N ASN N 233 " pdb=" CA ASN N 233 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C ARG H 232 " pdb=" N ASN H 233 " pdb=" CA ASN H 233 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C ARG J 232 " pdb=" N ASN J 233 " pdb=" CA ASN J 233 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C ARG M 232 " pdb=" N ASN M 233 " pdb=" CA ASN M 233 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 ... (remaining 37312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.89: 13866 13.89 - 27.78: 2052 27.78 - 41.67: 635 41.67 - 55.56: 142 55.56 - 69.46: 70 Dihedral angle restraints: 16765 sinusoidal: 6664 harmonic: 10101 Sorted by residual: dihedral pdb=" CA ASN M 223 " pdb=" C ASN M 223 " pdb=" N ASP M 224 " pdb=" CA ASP M 224 " ideal model delta harmonic sigma weight residual 180.00 149.52 30.48 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA ASN L 223 " pdb=" C ASN L 223 " pdb=" N ASP L 224 " pdb=" CA ASP L 224 " ideal model delta harmonic sigma weight residual 180.00 149.54 30.46 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA ASN I 223 " pdb=" C ASN I 223 " pdb=" N ASP I 224 " pdb=" CA ASP I 224 " ideal model delta harmonic sigma weight residual 180.00 149.55 30.45 0 5.00e+00 4.00e-02 3.71e+01 ... (remaining 16762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3360 0.069 - 0.138: 760 0.138 - 0.207: 87 0.207 - 0.276: 7 0.276 - 0.345: 7 Chirality restraints: 4221 Sorted by residual: chirality pdb=" CB VAL L 686 " pdb=" CA VAL L 686 " pdb=" CG1 VAL L 686 " pdb=" CG2 VAL L 686 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB VAL H 686 " pdb=" CA VAL H 686 " pdb=" CG1 VAL H 686 " pdb=" CG2 VAL H 686 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB VAL M 686 " pdb=" CA VAL M 686 " pdb=" CG1 VAL M 686 " pdb=" CG2 VAL M 686 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 4218 not shown) Planarity restraints: 4858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE L 510 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C ILE L 510 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE L 510 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP L 511 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE I 510 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" C ILE I 510 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE I 510 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP I 511 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 510 " -0.014 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C ILE H 510 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE H 510 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP H 511 " -0.016 2.00e-02 2.50e+03 ... (remaining 4855 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2681 2.73 - 3.27: 25657 3.27 - 3.82: 43681 3.82 - 4.36: 48758 4.36 - 4.90: 84176 Nonbonded interactions: 204953 Sorted by model distance: nonbonded pdb=" O ALA J 315 " pdb=" OG SER K 380 " model vdw 2.188 2.440 nonbonded pdb=" O TYR J 674 " pdb=" OH TYR J 697 " model vdw 2.246 2.440 nonbonded pdb=" O TYR H 674 " pdb=" OH TYR H 697 " model vdw 2.246 2.440 nonbonded pdb=" O TYR K 674 " pdb=" OH TYR K 697 " model vdw 2.246 2.440 nonbonded pdb=" O TYR M 674 " pdb=" OH TYR M 697 " model vdw 2.246 2.440 ... (remaining 204948 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 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.310 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 71.860 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.007 0.052 27517 Z= 0.471 Angle : 0.959 11.819 37317 Z= 0.525 Chirality : 0.059 0.345 4221 Planarity : 0.006 0.065 4858 Dihedral : 15.348 69.455 10297 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 1.60 % Allowed : 12.62 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.31 (0.11), residues: 3423 helix: -3.35 (0.15), residues: 441 sheet: -1.65 (0.14), residues: 1008 loop : -3.58 (0.11), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 632 HIS 0.020 0.013 HIS N 314 PHE 0.025 0.003 PHE I 487 TYR 0.023 0.003 TYR K 261 ARG 0.005 0.001 ARG K 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 229 time to evaluate : 3.038 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: H 414 LEU cc_start: 0.8824 (tp) cc_final: 0.8620 (tt) REVERT: H 452 MET cc_start: 0.6164 (ptt) cc_final: 0.5850 (ptt) REVERT: H 539 GLU cc_start: 0.8498 (pp20) cc_final: 0.8056 (tm-30) REVERT: I 736 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7951 (mp) REVERT: J 539 GLU cc_start: 0.8364 (pp20) cc_final: 0.8033 (tm-30) REVERT: J 540 ASP cc_start: 0.8297 (t70) cc_final: 0.8083 (t0) REVERT: K 553 LYS cc_start: 0.7802 (tttm) cc_final: 0.7399 (mmtp) REVERT: K 636 ASN cc_start: 0.6049 (OUTLIER) cc_final: 0.4802 (p0) REVERT: K 657 LYS cc_start: 0.7987 (mttt) cc_final: 0.7683 (pttt) REVERT: K 736 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7703 (mp) REVERT: M 453 ASP cc_start: 0.9007 (t0) cc_final: 0.8714 (t0) REVERT: M 482 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: M 625 TYR cc_start: 0.7926 (t80) cc_final: 0.7712 (t80) REVERT: M 709 TYR cc_start: 0.8339 (m-80) cc_final: 0.7931 (m-80) REVERT: M 736 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7847 (mp) REVERT: N 386 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8182 (p) REVERT: N 403 MET cc_start: 0.8937 (tpp) cc_final: 0.8515 (ttm) REVERT: N 482 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: N 736 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7755 (mp) outliers start: 49 outliers final: 8 residues processed: 278 average time/residue: 0.3754 time to fit residues: 166.5621 Evaluate side-chains 155 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 9.9990 chunk 259 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 88 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 268 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 163 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 425 GLN H 427 ASN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 482 GLN H 523 ASN H 648 ASN I 425 GLN I 427 ASN I 523 ASN I 648 ASN I 720 ASN J 425 GLN J 427 ASN J 523 ASN J 648 ASN K 425 GLN K 427 ASN K 454 GLN K 523 ASN K 648 ASN ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 425 GLN L 427 ASN L 648 ASN M 425 GLN M 427 ASN M 648 ASN N 425 GLN N 463 ASN N 523 ASN N 648 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27517 Z= 0.191 Angle : 0.641 9.201 37317 Z= 0.337 Chirality : 0.044 0.156 4221 Planarity : 0.004 0.042 4858 Dihedral : 6.263 25.625 3696 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.29 % Allowed : 4.73 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.13), residues: 3423 helix: -2.46 (0.19), residues: 462 sheet: -0.95 (0.15), residues: 938 loop : -3.11 (0.12), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 503 HIS 0.007 0.004 HIS N 314 PHE 0.011 0.001 PHE L 711 TYR 0.013 0.001 TYR H 625 ARG 0.004 0.000 ARG K 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 253 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 452 MET cc_start: 0.6143 (ptt) cc_final: 0.5826 (ptt) REVERT: J 452 MET cc_start: 0.6138 (ptt) cc_final: 0.5725 (ptt) REVERT: J 540 ASP cc_start: 0.8299 (t70) cc_final: 0.8054 (t0) REVERT: J 710 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6655 (tp30) REVERT: K 657 LYS cc_start: 0.7919 (mttt) cc_final: 0.7639 (pttt) REVERT: K 660 MET cc_start: 0.6129 (mpp) cc_final: 0.5530 (mpp) REVERT: K 736 LEU cc_start: 0.8112 (mp) cc_final: 0.7482 (tt) REVERT: L 425 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: L 453 ASP cc_start: 0.8788 (t0) cc_final: 0.8421 (t70) REVERT: L 539 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8846 (tm-30) REVERT: L 620 THR cc_start: 0.6862 (p) cc_final: 0.6572 (p) REVERT: L 625 TYR cc_start: 0.7702 (t80) cc_final: 0.7466 (t80) REVERT: L 710 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6632 (tp30) REVERT: L 736 LEU cc_start: 0.8295 (mp) cc_final: 0.7782 (tt) REVERT: M 453 ASP cc_start: 0.8931 (t0) cc_final: 0.8548 (t0) REVERT: M 625 TYR cc_start: 0.7745 (t80) cc_final: 0.7242 (t80) REVERT: M 709 TYR cc_start: 0.8276 (m-80) cc_final: 0.8015 (m-10) REVERT: N 403 MET cc_start: 0.9010 (tpp) cc_final: 0.8278 (ttm) REVERT: N 539 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8471 (tm-30) REVERT: N 620 THR cc_start: 0.7025 (p) cc_final: 0.6767 (p) REVERT: N 736 LEU cc_start: 0.8215 (mp) cc_final: 0.7838 (tt) outliers start: 9 outliers final: 3 residues processed: 262 average time/residue: 0.3821 time to fit residues: 162.0400 Evaluate side-chains 161 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 259 optimal weight: 0.5980 chunk 212 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 312 optimal weight: 0.0060 chunk 337 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 309 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 250 optimal weight: 0.9980 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 425 GLN H 523 ASN I 523 ASN ** J 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 523 ASN ** K 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 523 ASN ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 GLN N 425 GLN N 427 ASN N 523 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27517 Z= 0.189 Angle : 0.594 6.022 37317 Z= 0.318 Chirality : 0.043 0.155 4221 Planarity : 0.004 0.041 4858 Dihedral : 5.860 23.389 3696 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.13), residues: 3423 helix: -1.86 (0.22), residues: 441 sheet: -0.81 (0.16), residues: 952 loop : -2.97 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 503 HIS 0.008 0.005 HIS I 314 PHE 0.011 0.002 PHE M 281 TYR 0.017 0.001 TYR L 271 ARG 0.004 0.000 ARG L 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 452 MET cc_start: 0.6001 (ptt) cc_final: 0.5797 (ptt) REVERT: H 710 GLU cc_start: 0.6341 (mt-10) cc_final: 0.5732 (tp30) REVERT: I 553 LYS cc_start: 0.8601 (tttt) cc_final: 0.8384 (tttt) REVERT: I 660 MET cc_start: 0.6506 (mpp) cc_final: 0.6250 (mpp) REVERT: J 452 MET cc_start: 0.6035 (ptt) cc_final: 0.5749 (ptt) REVERT: J 660 MET cc_start: 0.7005 (mpp) cc_final: 0.6494 (mpp) REVERT: J 710 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6479 (tp30) REVERT: K 452 MET cc_start: 0.5096 (ptt) cc_final: 0.4888 (ptt) REVERT: K 657 LYS cc_start: 0.7924 (mttt) cc_final: 0.7665 (pttt) REVERT: K 660 MET cc_start: 0.5946 (mpp) cc_final: 0.5524 (mpp) REVERT: L 453 ASP cc_start: 0.8910 (t0) cc_final: 0.8473 (t70) REVERT: L 462 ILE cc_start: 0.8775 (tt) cc_final: 0.8566 (mt) REVERT: L 539 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8822 (tm-30) REVERT: L 620 THR cc_start: 0.6790 (p) cc_final: 0.6288 (p) REVERT: L 625 TYR cc_start: 0.7829 (t80) cc_final: 0.7496 (t80) REVERT: L 736 LEU cc_start: 0.8330 (mp) cc_final: 0.7663 (tt) REVERT: M 452 MET cc_start: 0.5291 (ptt) cc_final: 0.4946 (ptt) REVERT: M 453 ASP cc_start: 0.8792 (t0) cc_final: 0.8482 (t0) REVERT: M 460 ILE cc_start: 0.8243 (tp) cc_final: 0.7963 (pt) REVERT: M 625 TYR cc_start: 0.7761 (t80) cc_final: 0.7295 (t80) REVERT: M 709 TYR cc_start: 0.8331 (m-80) cc_final: 0.7933 (m-10) REVERT: N 403 MET cc_start: 0.8865 (tpp) cc_final: 0.8246 (ttm) REVERT: N 453 ASP cc_start: 0.8873 (t0) cc_final: 0.8528 (t70) REVERT: N 620 THR cc_start: 0.7271 (p) cc_final: 0.7015 (p) REVERT: N 710 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6130 (tp30) REVERT: N 736 LEU cc_start: 0.8271 (mp) cc_final: 0.7929 (tt) outliers start: 3 outliers final: 0 residues processed: 255 average time/residue: 0.3744 time to fit residues: 152.4835 Evaluate side-chains 153 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 313 optimal weight: 6.9990 chunk 331 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 411 ASN ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 454 GLN M 411 ASN M 425 GLN N 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27517 Z= 0.241 Angle : 0.622 6.863 37317 Z= 0.332 Chirality : 0.044 0.166 4221 Planarity : 0.004 0.044 4858 Dihedral : 5.695 22.291 3696 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.13), residues: 3423 helix: -1.48 (0.23), residues: 406 sheet: -0.73 (0.16), residues: 966 loop : -2.82 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 503 HIS 0.010 0.006 HIS I 314 PHE 0.016 0.002 PHE M 487 TYR 0.021 0.002 TYR M 271 ARG 0.006 0.001 ARG K 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 710 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6019 (tp30) REVERT: I 403 MET cc_start: 0.8406 (tpp) cc_final: 0.8104 (tpt) REVERT: I 620 THR cc_start: 0.7449 (p) cc_final: 0.7169 (p) REVERT: I 625 TYR cc_start: 0.7347 (t80) cc_final: 0.7142 (t80) REVERT: I 660 MET cc_start: 0.6265 (mpp) cc_final: 0.5867 (mpp) REVERT: I 736 LEU cc_start: 0.8423 (mp) cc_final: 0.7848 (tt) REVERT: J 539 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8753 (tm-30) REVERT: J 660 MET cc_start: 0.6889 (mpp) cc_final: 0.6405 (mpp) REVERT: J 710 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6521 (tp30) REVERT: K 609 MET cc_start: 0.7340 (mtt) cc_final: 0.7103 (mtp) REVERT: K 620 THR cc_start: 0.6852 (p) cc_final: 0.6333 (p) REVERT: K 660 MET cc_start: 0.5892 (mpp) cc_final: 0.5452 (mpp) REVERT: K 708 SER cc_start: 0.8299 (p) cc_final: 0.7959 (m) REVERT: K 736 LEU cc_start: 0.8092 (mp) cc_final: 0.7310 (tt) REVERT: L 453 ASP cc_start: 0.8761 (t0) cc_final: 0.8201 (t70) REVERT: L 462 ILE cc_start: 0.8529 (tt) cc_final: 0.8291 (mt) REVERT: L 539 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8733 (tm-30) REVERT: L 609 MET cc_start: 0.7235 (ttm) cc_final: 0.6745 (ttm) REVERT: L 620 THR cc_start: 0.6703 (p) cc_final: 0.6348 (p) REVERT: L 625 TYR cc_start: 0.7815 (t80) cc_final: 0.7539 (t80) REVERT: L 736 LEU cc_start: 0.8231 (mp) cc_final: 0.7463 (tt) REVERT: M 453 ASP cc_start: 0.8881 (t0) cc_final: 0.8534 (t0) REVERT: M 625 TYR cc_start: 0.7836 (t80) cc_final: 0.7327 (t80) REVERT: M 708 SER cc_start: 0.8124 (p) cc_final: 0.7819 (m) REVERT: M 709 TYR cc_start: 0.8360 (m-80) cc_final: 0.7784 (m-10) REVERT: N 403 MET cc_start: 0.8698 (tpp) cc_final: 0.8056 (ttm) REVERT: N 455 PHE cc_start: 0.7665 (m-10) cc_final: 0.7090 (m-10) REVERT: N 620 THR cc_start: 0.6911 (p) cc_final: 0.6629 (p) REVERT: N 710 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6136 (tp30) REVERT: N 736 LEU cc_start: 0.8439 (mp) cc_final: 0.8026 (tt) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.3593 time to fit residues: 139.0920 Evaluate side-chains 160 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 0.0970 chunk 188 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 229 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 GLN ** J 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 454 GLN ** K 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 411 ASN M 425 GLN ** N 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27517 Z= 0.165 Angle : 0.565 6.095 37317 Z= 0.300 Chirality : 0.043 0.203 4221 Planarity : 0.003 0.031 4858 Dihedral : 5.365 21.265 3696 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.10 % Allowed : 3.00 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.13), residues: 3423 helix: -1.22 (0.24), residues: 399 sheet: -0.51 (0.16), residues: 966 loop : -2.74 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 632 HIS 0.005 0.002 HIS I 314 PHE 0.008 0.001 PHE M 487 TYR 0.013 0.001 TYR N 271 ARG 0.003 0.000 ARG K 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 243 time to evaluate : 3.450 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: H 620 THR cc_start: 0.6879 (p) cc_final: 0.6674 (p) REVERT: H 710 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6146 (tp30) REVERT: H 736 LEU cc_start: 0.8551 (mp) cc_final: 0.8328 (mp) REVERT: I 304 MET cc_start: 0.8765 (tpt) cc_final: 0.8555 (tpp) REVERT: I 403 MET cc_start: 0.8431 (tpp) cc_final: 0.8053 (tpt) REVERT: I 620 THR cc_start: 0.7816 (p) cc_final: 0.7566 (p) REVERT: I 625 TYR cc_start: 0.7350 (t80) cc_final: 0.7078 (t80) REVERT: I 660 MET cc_start: 0.6252 (mpp) cc_final: 0.5888 (mpp) REVERT: I 736 LEU cc_start: 0.8324 (mp) cc_final: 0.7739 (tt) REVERT: J 660 MET cc_start: 0.6821 (mpp) cc_final: 0.6420 (mpp) REVERT: J 710 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6252 (tp30) REVERT: K 620 THR cc_start: 0.6772 (p) cc_final: 0.6393 (p) REVERT: K 660 MET cc_start: 0.5820 (mpp) cc_final: 0.5495 (mpp) REVERT: K 708 SER cc_start: 0.8541 (p) cc_final: 0.8139 (m) REVERT: K 736 LEU cc_start: 0.8323 (mp) cc_final: 0.7473 (tt) REVERT: L 453 ASP cc_start: 0.8753 (t0) cc_final: 0.8121 (t70) REVERT: L 539 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8696 (tm-30) REVERT: L 620 THR cc_start: 0.6730 (p) cc_final: 0.6276 (p) REVERT: L 625 TYR cc_start: 0.7754 (t80) cc_final: 0.7536 (t80) REVERT: L 668 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7798 (ptp-110) REVERT: L 708 SER cc_start: 0.8484 (p) cc_final: 0.8226 (m) REVERT: L 736 LEU cc_start: 0.8217 (mp) cc_final: 0.7467 (tt) REVERT: M 453 ASP cc_start: 0.8811 (t0) cc_final: 0.8453 (t0) REVERT: M 625 TYR cc_start: 0.7804 (t80) cc_final: 0.7311 (t80) REVERT: M 708 SER cc_start: 0.8230 (p) cc_final: 0.7951 (m) REVERT: M 709 TYR cc_start: 0.8382 (m-80) cc_final: 0.7921 (m-10) REVERT: N 403 MET cc_start: 0.8655 (tpp) cc_final: 0.8107 (ttm) REVERT: N 620 THR cc_start: 0.6933 (p) cc_final: 0.6648 (p) REVERT: N 708 SER cc_start: 0.8536 (p) cc_final: 0.8115 (m) REVERT: N 710 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6062 (tp30) REVERT: N 736 LEU cc_start: 0.8694 (mp) cc_final: 0.8138 (tt) outliers start: 3 outliers final: 0 residues processed: 246 average time/residue: 0.3625 time to fit residues: 146.0644 Evaluate side-chains 156 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 331 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 454 GLN ** J 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 454 GLN ** N 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 27517 Z= 0.367 Angle : 0.705 7.201 37317 Z= 0.377 Chirality : 0.047 0.262 4221 Planarity : 0.004 0.047 4858 Dihedral : 5.952 23.442 3696 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.13), residues: 3423 helix: -1.34 (0.22), residues: 392 sheet: -0.79 (0.16), residues: 1015 loop : -2.79 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 245 HIS 0.016 0.009 HIS H 314 PHE 0.025 0.003 PHE N 619 TYR 0.027 0.002 TYR N 271 ARG 0.009 0.001 ARG K 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 466 GLN cc_start: 0.7907 (mp10) cc_final: 0.7218 (mp10) REVERT: H 710 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6055 (tp30) REVERT: I 553 LYS cc_start: 0.8115 (tttt) cc_final: 0.7754 (mmtt) REVERT: I 625 TYR cc_start: 0.7445 (t80) cc_final: 0.7222 (t80) REVERT: I 660 MET cc_start: 0.6214 (mpp) cc_final: 0.5789 (mpp) REVERT: J 625 TYR cc_start: 0.7610 (t80) cc_final: 0.7275 (t80) REVERT: J 710 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7011 (tp30) REVERT: K 553 LYS cc_start: 0.8326 (tttt) cc_final: 0.7784 (mmtt) REVERT: K 620 THR cc_start: 0.6937 (p) cc_final: 0.6403 (p) REVERT: K 660 MET cc_start: 0.6109 (mpp) cc_final: 0.5658 (mpp) REVERT: K 708 SER cc_start: 0.8292 (p) cc_final: 0.7869 (m) REVERT: K 736 LEU cc_start: 0.8166 (mp) cc_final: 0.7250 (tt) REVERT: L 452 MET cc_start: 0.5046 (ptt) cc_final: 0.4804 (ptt) REVERT: L 453 ASP cc_start: 0.8816 (t0) cc_final: 0.8191 (t70) REVERT: L 539 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8662 (tm-30) REVERT: L 620 THR cc_start: 0.6829 (p) cc_final: 0.6618 (p) REVERT: L 625 TYR cc_start: 0.7812 (t80) cc_final: 0.7575 (t80) REVERT: L 668 ARG cc_start: 0.7906 (mtp180) cc_final: 0.7689 (ptp90) REVERT: M 453 ASP cc_start: 0.8788 (t0) cc_final: 0.8533 (t70) REVERT: M 625 TYR cc_start: 0.7893 (t80) cc_final: 0.7321 (t80) REVERT: M 709 TYR cc_start: 0.8419 (m-80) cc_final: 0.7991 (m-10) REVERT: N 403 MET cc_start: 0.8677 (tpp) cc_final: 0.7901 (ttm) REVERT: N 453 ASP cc_start: 0.8844 (t0) cc_final: 0.8629 (t0) REVERT: N 710 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6074 (tp30) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3635 time to fit residues: 121.9455 Evaluate side-chains 140 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 242 optimal weight: 0.0040 chunk 187 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 330 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 GLN N 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27517 Z= 0.248 Angle : 0.630 7.619 37317 Z= 0.333 Chirality : 0.045 0.208 4221 Planarity : 0.004 0.082 4858 Dihedral : 5.767 23.678 3696 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.07 % Allowed : 1.57 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.13), residues: 3423 helix: -1.33 (0.23), residues: 392 sheet: -0.67 (0.16), residues: 973 loop : -2.71 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 245 HIS 0.010 0.005 HIS N 314 PHE 0.015 0.002 PHE M 487 TYR 0.019 0.001 TYR K 271 ARG 0.007 0.001 ARG K 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 3.300 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: H 466 GLN cc_start: 0.7863 (mp10) cc_final: 0.7166 (mp10) REVERT: H 660 MET cc_start: 0.6631 (mpp) cc_final: 0.6315 (mpp) REVERT: H 710 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6060 (tp30) REVERT: I 553 LYS cc_start: 0.8051 (tttt) cc_final: 0.7690 (mmtt) REVERT: J 625 TYR cc_start: 0.7564 (t80) cc_final: 0.7196 (t80) REVERT: J 710 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6905 (tp30) REVERT: K 553 LYS cc_start: 0.8301 (tttt) cc_final: 0.7631 (mttt) REVERT: K 620 THR cc_start: 0.6889 (p) cc_final: 0.6613 (p) REVERT: K 660 MET cc_start: 0.6031 (mpp) cc_final: 0.5585 (mpp) REVERT: K 708 SER cc_start: 0.8348 (p) cc_final: 0.7938 (m) REVERT: K 736 LEU cc_start: 0.8264 (mp) cc_final: 0.7510 (tt) REVERT: L 452 MET cc_start: 0.5016 (ptt) cc_final: 0.4816 (ptt) REVERT: L 539 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8725 (tm-30) REVERT: L 625 TYR cc_start: 0.7763 (t80) cc_final: 0.7524 (t80) REVERT: L 668 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7724 (ptp90) REVERT: M 453 ASP cc_start: 0.8725 (t0) cc_final: 0.8505 (t70) REVERT: M 625 TYR cc_start: 0.7873 (t80) cc_final: 0.7286 (t80) REVERT: M 709 TYR cc_start: 0.8302 (m-80) cc_final: 0.8087 (m-10) REVERT: N 403 MET cc_start: 0.8678 (tpp) cc_final: 0.7863 (ttm) REVERT: N 453 ASP cc_start: 0.8857 (t0) cc_final: 0.8610 (t0) REVERT: N 710 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6182 (tp30) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.3634 time to fit residues: 123.0759 Evaluate side-chains 144 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 259 optimal weight: 0.2980 chunk 300 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 425 GLN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 GLN M 636 ASN N 636 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27517 Z= 0.180 Angle : 0.593 6.256 37317 Z= 0.312 Chirality : 0.044 0.195 4221 Planarity : 0.003 0.036 4858 Dihedral : 5.379 23.008 3696 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 0.13 % Allowed : 1.11 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.14), residues: 3423 helix: -1.14 (0.24), residues: 392 sheet: -0.50 (0.16), residues: 973 loop : -2.63 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 375 HIS 0.006 0.002 HIS N 314 PHE 0.010 0.001 PHE L 580 TYR 0.015 0.001 TYR K 271 ARG 0.006 0.000 ARG N 668 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 466 GLN cc_start: 0.7860 (mp10) cc_final: 0.7182 (mp10) REVERT: H 709 TYR cc_start: 0.7943 (m-10) cc_final: 0.7521 (m-10) REVERT: H 736 LEU cc_start: 0.8472 (mp) cc_final: 0.7686 (tt) REVERT: I 553 LYS cc_start: 0.8277 (tttt) cc_final: 0.7666 (mmtt) REVERT: J 539 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8708 (tm-30) REVERT: J 625 TYR cc_start: 0.7663 (t80) cc_final: 0.7284 (t80) REVERT: J 710 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6920 (tp30) REVERT: K 453 ASP cc_start: 0.8615 (t70) cc_final: 0.8279 (t70) REVERT: K 553 LYS cc_start: 0.8289 (tttt) cc_final: 0.7735 (mttt) REVERT: K 620 THR cc_start: 0.6781 (p) cc_final: 0.6263 (p) REVERT: K 660 MET cc_start: 0.6008 (mpp) cc_final: 0.5555 (mpp) REVERT: K 708 SER cc_start: 0.8346 (p) cc_final: 0.7989 (m) REVERT: K 736 LEU cc_start: 0.8451 (mp) cc_final: 0.7767 (tt) REVERT: L 452 MET cc_start: 0.5543 (ptt) cc_final: 0.5340 (ptt) REVERT: L 453 ASP cc_start: 0.8593 (t0) cc_final: 0.8039 (t70) REVERT: L 539 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8703 (tm-30) REVERT: L 625 TYR cc_start: 0.7744 (t80) cc_final: 0.7514 (t80) REVERT: L 660 MET cc_start: 0.7171 (mpp) cc_final: 0.6452 (mpp) REVERT: M 625 TYR cc_start: 0.7856 (t80) cc_final: 0.7284 (t80) REVERT: M 636 ASN cc_start: 0.6845 (OUTLIER) cc_final: 0.5826 (t0) REVERT: N 403 MET cc_start: 0.8566 (tpp) cc_final: 0.8071 (ttm) REVERT: N 636 ASN cc_start: 0.5583 (OUTLIER) cc_final: 0.3984 (t0) REVERT: N 708 SER cc_start: 0.8673 (p) cc_final: 0.8254 (m) REVERT: N 710 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6031 (tp30) outliers start: 4 outliers final: 0 residues processed: 217 average time/residue: 0.3606 time to fit residues: 127.0575 Evaluate side-chains 146 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 0.0980 chunk 288 optimal weight: 20.0000 chunk 308 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 291 optimal weight: 8.9990 chunk 306 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 ASN ** I 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 636 ASN ** J 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 ASN ** K 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 GLN M 636 ASN ** N 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 636 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27517 Z= 0.340 Angle : 0.690 6.692 37317 Z= 0.367 Chirality : 0.046 0.204 4221 Planarity : 0.004 0.040 4858 Dihedral : 5.783 24.259 3696 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 0.20 % Allowed : 1.08 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.14), residues: 3423 helix: -1.31 (0.23), residues: 399 sheet: -0.59 (0.16), residues: 966 loop : -2.71 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 245 HIS 0.015 0.008 HIS N 314 PHE 0.030 0.002 PHE I 619 TYR 0.029 0.002 TYR M 628 ARG 0.007 0.001 ARG K 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 466 GLN cc_start: 0.7876 (mp10) cc_final: 0.7148 (mp10) REVERT: H 636 ASN cc_start: 0.6576 (OUTLIER) cc_final: 0.5214 (t0) REVERT: H 671 PHE cc_start: 0.8007 (t80) cc_final: 0.7780 (t80) REVERT: I 636 ASN cc_start: 0.5787 (OUTLIER) cc_final: 0.4760 (t0) REVERT: J 313 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7150 (tt0) REVERT: J 625 TYR cc_start: 0.7682 (t80) cc_final: 0.7326 (t80) REVERT: J 636 ASN cc_start: 0.5316 (OUTLIER) cc_final: 0.4228 (t0) REVERT: J 710 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6993 (tp30) REVERT: K 403 MET cc_start: 0.8879 (tpp) cc_final: 0.8607 (ttm) REVERT: K 453 ASP cc_start: 0.8399 (t70) cc_final: 0.8057 (t70) REVERT: K 553 LYS cc_start: 0.8240 (tttt) cc_final: 0.7657 (mttt) REVERT: K 660 MET cc_start: 0.5974 (mpp) cc_final: 0.5542 (mpp) REVERT: K 708 SER cc_start: 0.8528 (p) cc_final: 0.8096 (m) REVERT: L 452 MET cc_start: 0.5639 (ptt) cc_final: 0.5416 (ptt) REVERT: L 466 GLN cc_start: 0.8175 (mp10) cc_final: 0.7492 (mp10) REVERT: L 539 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8642 (tm-30) REVERT: L 625 TYR cc_start: 0.7776 (t80) cc_final: 0.7556 (t80) REVERT: L 660 MET cc_start: 0.7163 (mpp) cc_final: 0.6444 (mpp) REVERT: M 625 TYR cc_start: 0.7898 (t80) cc_final: 0.7289 (t80) REVERT: M 636 ASN cc_start: 0.6481 (OUTLIER) cc_final: 0.5329 (t0) REVERT: N 403 MET cc_start: 0.8673 (tpp) cc_final: 0.7873 (ttm) REVERT: N 453 ASP cc_start: 0.8842 (t0) cc_final: 0.8573 (t0) REVERT: N 636 ASN cc_start: 0.5707 (OUTLIER) cc_final: 0.4238 (t0) outliers start: 6 outliers final: 0 residues processed: 186 average time/residue: 0.3595 time to fit residues: 109.1888 Evaluate side-chains 136 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 chunk 314 optimal weight: 0.8980 chunk 272 optimal weight: 8.9990 chunk 28 optimal weight: 0.0070 chunk 210 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 382 ASN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 ASN ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 636 ASN ** J 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 636 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27517 Z= 0.179 Angle : 0.598 6.419 37317 Z= 0.313 Chirality : 0.044 0.205 4221 Planarity : 0.003 0.038 4858 Dihedral : 5.411 23.802 3696 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.13 % Allowed : 0.42 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.14), residues: 3423 helix: -1.12 (0.24), residues: 392 sheet: -0.39 (0.16), residues: 966 loop : -2.58 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 632 HIS 0.005 0.002 HIS N 314 PHE 0.021 0.001 PHE I 619 TYR 0.016 0.001 TYR N 625 ARG 0.004 0.000 ARG I 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 466 GLN cc_start: 0.7872 (mp10) cc_final: 0.7158 (mp10) REVERT: H 620 THR cc_start: 0.6859 (p) cc_final: 0.6644 (p) REVERT: H 636 ASN cc_start: 0.6801 (OUTLIER) cc_final: 0.5289 (t0) REVERT: H 736 LEU cc_start: 0.8465 (mp) cc_final: 0.7705 (tt) REVERT: I 553 LYS cc_start: 0.8316 (tttt) cc_final: 0.7726 (mttt) REVERT: I 636 ASN cc_start: 0.5910 (OUTLIER) cc_final: 0.4825 (t0) REVERT: J 313 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6924 (tt0) REVERT: J 539 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8710 (tm-30) REVERT: J 625 TYR cc_start: 0.7687 (t80) cc_final: 0.7397 (t80) REVERT: J 710 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6974 (tp30) REVERT: K 453 ASP cc_start: 0.8664 (t70) cc_final: 0.8294 (t70) REVERT: K 553 LYS cc_start: 0.8204 (tttt) cc_final: 0.7627 (mttt) REVERT: K 660 MET cc_start: 0.5994 (mpp) cc_final: 0.5578 (mpp) REVERT: K 708 SER cc_start: 0.8487 (p) cc_final: 0.8115 (m) REVERT: L 452 MET cc_start: 0.5539 (ptt) cc_final: 0.5330 (ptt) REVERT: L 539 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8703 (tm-30) REVERT: L 620 THR cc_start: 0.6762 (p) cc_final: 0.6519 (p) REVERT: L 697 TYR cc_start: 0.6786 (t80) cc_final: 0.6527 (t80) REVERT: M 609 MET cc_start: 0.7592 (ttm) cc_final: 0.7378 (ttm) REVERT: M 625 TYR cc_start: 0.7803 (t80) cc_final: 0.7267 (t80) REVERT: M 636 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.5219 (t0) REVERT: M 708 SER cc_start: 0.8289 (p) cc_final: 0.8007 (m) REVERT: M 736 LEU cc_start: 0.8431 (mp) cc_final: 0.7949 (tt) REVERT: N 403 MET cc_start: 0.8584 (tpp) cc_final: 0.8084 (ttm) outliers start: 4 outliers final: 0 residues processed: 200 average time/residue: 0.3605 time to fit residues: 119.4110 Evaluate side-chains 146 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 239 optimal weight: 0.1980 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 425 GLN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 ASN ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 636 ASN ** J 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 ASN ** K 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 636 ASN N 636 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.110592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090073 restraints weight = 77022.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.088603 restraints weight = 78555.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089398 restraints weight = 76680.145| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27517 Z= 0.192 Angle : 0.594 6.309 37317 Z= 0.311 Chirality : 0.044 0.234 4221 Planarity : 0.003 0.039 4858 Dihedral : 5.313 24.815 3696 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.20 % Allowed : 0.29 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.14), residues: 3423 helix: -1.00 (0.24), residues: 392 sheet: -0.32 (0.16), residues: 966 loop : -2.58 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 632 HIS 0.007 0.003 HIS J 314 PHE 0.018 0.001 PHE I 619 TYR 0.015 0.001 TYR N 601 ARG 0.005 0.000 ARG I 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4064.83 seconds wall clock time: 76 minutes 41.73 seconds (4601.73 seconds total)