Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 11:09:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/10_2023/6okt_20104.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/10_2023/6okt_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_20104/10_2023/6okt_20104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/10_2023/6okt_20104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/10_2023/6okt_20104.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okt_20104/10_2023/6okt_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-1.21rc1-5097/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: 13.25, per 1000 atoms: 0.49 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: 9.42 Conformation dependent library (CDL) restraints added in 3.9 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: 2.77 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: 9.00 Time building geometry restraints manager: 10.27 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.940 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 64.360 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.150 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.020 ------------------------------------------------------------------------------- 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 *********************** 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 : 3.436 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 outliers start: 49 outliers final: 8 residues processed: 278 average time/residue: 0.4015 time to fit residues: 178.3921 Evaluate side-chains 143 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 2.943 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2208 time to fit residues: 7.3630 ------------------------------------------------------------------------------- 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: 10.0000 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: 2.9990 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: 1.1182 ------------------------------------------------------------------------------- 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 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 K 720 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: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27517 Z= 0.176 Angle : 0.633 8.951 37317 Z= 0.334 Chirality : 0.044 0.159 4221 Planarity : 0.004 0.041 4858 Dihedral : 6.213 25.666 3696 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.29 % Allowed : 4.53 % Favored : 95.17 % 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: -3.47 (0.13), residues: 3423 helix: -2.46 (0.19), residues: 462 sheet: -0.92 (0.16), residues: 938 loop : -3.11 (0.12), residues: 2023 *********************** 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 266 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 257 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 266 average time/residue: 0.3998 time to fit residues: 171.9642 Evaluate side-chains 147 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 2.969 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2865 time to fit residues: 6.0283 ------------------------------------------------------------------------------- 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: 0.0970 chunk 96 optimal weight: 20.0000 chunk 259 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 312 optimal weight: 0.1980 chunk 337 optimal weight: 0.0970 chunk 277 optimal weight: 10.0000 chunk 309 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 overall best weight: 1.2780 ------------------------------------------------------------------------------- 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 425 GLN ** J 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 523 ASN K 523 ASN ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 427 ASN N 523 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2102 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= 0.172 Angle : 0.591 7.660 37317 Z= 0.314 Chirality : 0.043 0.167 4221 Planarity : 0.004 0.038 4858 Dihedral : 5.737 23.679 3696 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.74 % 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: -3.13 (0.13), residues: 3423 helix: -1.95 (0.22), residues: 455 sheet: -0.69 (0.16), residues: 938 loop : -2.95 (0.13), residues: 2030 *********************** 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 251 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 251 average time/residue: 0.3967 time to fit residues: 159.0976 Evaluate side-chains 143 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 3.445 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2823 time to fit residues: 4.6588 ------------------------------------------------------------------------------- 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: 0.9980 chunk 234 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 313 optimal weight: 10.0000 chunk 331 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 296 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 454 GLN ** J 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 432 ASN ** 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** ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 454 GLN ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 411 ASN M 454 GLN ** N 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27517 Z= 0.312 Angle : 0.681 6.781 37317 Z= 0.365 Chirality : 0.046 0.212 4221 Planarity : 0.004 0.045 4858 Dihedral : 5.900 23.173 3696 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -2.99 (0.13), residues: 3423 helix: -1.53 (0.22), residues: 406 sheet: -0.82 (0.16), residues: 952 loop : -2.82 (0.13), residues: 2065 *********************** 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 208 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.3740 time to fit residues: 127.6189 Evaluate side-chains 133 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4564 ------------------------------------------------------------------------------- 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: 0.9980 chunk 188 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 282 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 297 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 411 ASN M 425 GLN N 425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 27517 Z= 0.187 Angle : 0.585 6.980 37317 Z= 0.310 Chirality : 0.043 0.197 4221 Planarity : 0.003 0.032 4858 Dihedral : 5.511 21.973 3696 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.58 % 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: -2.78 (0.13), residues: 3423 helix: -1.28 (0.23), residues: 399 sheet: -0.58 (0.16), residues: 952 loop : -2.74 (0.13), residues: 2072 *********************** 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 223 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 223 average time/residue: 0.3552 time to fit residues: 131.2312 Evaluate side-chains 144 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 3.280 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4759 ------------------------------------------------------------------------------- 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: 4.9990 chunk 298 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 275 optimal weight: 0.0870 chunk 153 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 overall best weight: 3.9764 ------------------------------------------------------------------------------- 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** ** J 314 HIS ** 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** ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27517 Z= 0.336 Angle : 0.679 7.992 37317 Z= 0.362 Chirality : 0.046 0.258 4221 Planarity : 0.004 0.041 4858 Dihedral : 5.816 22.898 3696 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -2.86 (0.13), residues: 3423 helix: -1.36 (0.23), residues: 392 sheet: -0.72 (0.16), residues: 994 loop : -2.77 (0.13), residues: 2037 *********************** 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 198 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3693 time to fit residues: 120.7331 Evaluate side-chains 132 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4925 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 0.9990 chunk 189 optimal weight: 0.2980 chunk 242 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 330 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 454 GLN ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 GLN N 425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27517 Z= 0.181 Angle : 0.592 6.553 37317 Z= 0.311 Chirality : 0.044 0.214 4221 Planarity : 0.003 0.033 4858 Dihedral : 5.474 22.235 3696 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.10 % Allowed : 1.50 % Favored : 98.40 % 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: -2.66 (0.14), residues: 3423 helix: -1.17 (0.24), residues: 392 sheet: -0.50 (0.16), residues: 952 loop : -2.65 (0.13), residues: 2079 *********************** 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 207 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 207 average time/residue: 0.3731 time to fit residues: 125.7501 Evaluate side-chains 130 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.136 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1434 ------------------------------------------------------------------------------- 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: 0.9980 chunk 132 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 99 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 259 optimal weight: 0.1980 chunk 300 optimal weight: 8.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 636 ASN I 636 ASN ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 ASN ** K 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 636 ASN N 636 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27517 Z= 0.159 Angle : 0.584 6.443 37317 Z= 0.304 Chirality : 0.043 0.253 4221 Planarity : 0.003 0.037 4858 Dihedral : 5.168 21.224 3696 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.16 % Allowed : 0.62 % Favored : 99.22 % 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: -2.49 (0.14), residues: 3423 helix: -0.97 (0.24), residues: 392 sheet: -0.46 (0.16), residues: 980 loop : -2.54 (0.13), residues: 2051 *********************** 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 210 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 205 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 210 average time/residue: 0.3691 time to fit residues: 128.0849 Evaluate side-chains 130 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5294 ------------------------------------------------------------------------------- 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: 9.9990 chunk 288 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 291 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 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** ** J 314 HIS ** 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** ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27517 Z= 0.366 Angle : 0.708 6.676 37317 Z= 0.377 Chirality : 0.047 0.234 4221 Planarity : 0.004 0.096 4858 Dihedral : 5.756 23.699 3696 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -2.70 (0.14), residues: 3423 helix: -1.18 (0.23), residues: 392 sheet: -0.57 (0.16), residues: 1001 loop : -2.71 (0.13), residues: 2030 *********************** 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 175 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3614 time to fit residues: 104.6883 Evaluate side-chains 124 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 3.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5166 ------------------------------------------------------------------------------- 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: 2.9990 chunk 198 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 341 optimal weight: 7.9990 chunk 314 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 chunk 28 optimal weight: 0.0170 chunk 210 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 425 GLN ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27517 Z= 0.168 Angle : 0.593 6.364 37317 Z= 0.310 Chirality : 0.044 0.222 4221 Planarity : 0.003 0.071 4858 Dihedral : 5.327 23.391 3696 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.07 % Allowed : 0.20 % Favored : 99.74 % 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: -2.48 (0.14), residues: 3423 helix: -1.06 (0.24), residues: 392 sheet: -0.41 (0.16), residues: 973 loop : -2.53 (0.13), residues: 2058 ********************** 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 188 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.3569 time to fit residues: 111.0152 Evaluate side-chains 130 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.928 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0837 ------------------------------------------------------------------------------- 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: 0.2980 chunk 83 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 114 optimal weight: 0.0030 chunk 279 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 239 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 482 GLN ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.113708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092717 restraints weight = 76158.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091561 restraints weight = 62475.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092325 restraints weight = 72353.390| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27517 Z= 0.144 Angle : 0.565 7.213 37317 Z= 0.290 Chirality : 0.043 0.203 4221 Planarity : 0.003 0.056 4858 Dihedral : 4.831 24.098 3696 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -2.29 (0.14), residues: 3423 helix: -0.75 (0.25), residues: 392 sheet: -0.27 (0.16), residues: 994 loop : -2.46 (0.13), residues: 2037 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3927.59 seconds wall clock time: 74 minutes 49.75 seconds (4489.75 seconds total)