Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 09:35:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/04_2023/7scn_25039.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/04_2023/7scn_25039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/04_2023/7scn_25039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/04_2023/7scn_25039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/04_2023/7scn_25039.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scn_25039/04_2023/7scn_25039.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 78 5.16 5 C 10806 2.51 5 N 2919 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17145 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "B" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "D" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "F" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "I" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain: "J" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 9.01, per 1000 atoms: 0.53 Number of scatterers: 17145 At special positions: 0 Unit cell: (124.2, 129.95, 147.2, 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 78 16.00 O 3342 8.00 N 2919 7.00 C 10806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.05 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.02 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.05 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS H 529 " - pdb=" SG CYS H 602 " distance=2.01 Simple disulfide: pdb=" SG CYS L 646 " - pdb=" SG CYS L 712 " distance=2.02 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 467 " distance=2.04 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.05 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.05 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 529 " - pdb=" SG CYS E 602 " distance=2.01 Simple disulfide: pdb=" SG CYS F 646 " - pdb=" SG CYS F 712 " distance=2.02 Simple disulfide: pdb=" SG CYS G 8 " - pdb=" SG CYS I 467 " distance=2.04 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 278 " distance=2.05 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 71 " distance=2.02 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 139 " distance=2.05 Simple disulfide: pdb=" SG CYS G 282 " - pdb=" SG CYS G 306 " distance=2.02 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 478 " distance=2.03 Simple disulfide: pdb=" SG CYS J 529 " - pdb=" SG CYS J 602 " distance=2.01 Simple disulfide: pdb=" SG CYS K 646 " - pdb=" SG CYS K 712 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 58 " " NAG A 402 " - " ASN A 27 " " NAG A 403 " - " ASN A 91 " " NAG A 404 " - " ASN A 129 " " NAG A 405 " - " ASN A 290 " " NAG C 401 " - " ASN C 58 " " NAG C 402 " - " ASN C 27 " " NAG C 403 " - " ASN C 91 " " NAG C 404 " - " ASN C 129 " " NAG C 405 " - " ASN C 290 " " NAG G 401 " - " ASN G 58 " " NAG G 402 " - " ASN G 27 " " NAG G 403 " - " ASN G 91 " " NAG G 404 " - " ASN G 129 " " NAG G 405 " - " ASN G 290 " Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 2.6 seconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 51 sheets defined 22.4% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.899A pdb=" N GLU A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU A 73 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.340A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 367 through 389 Processing helix chain 'B' and resid 404 through 457 removed outlier: 4.028A pdb=" N GLN B 455 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 488 through 503 removed outlier: 3.826A pdb=" N TYR B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU B 494 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 535 through 539 Processing helix chain 'H' and resid 568 through 571 Processing helix chain 'L' and resid 653 through 655 No H-bonds generated for 'chain 'L' and resid 653 through 655' Processing helix chain 'L' and resid 703 through 707 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.898A pdb=" N GLU C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU C 73 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.341A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 367 through 389 Processing helix chain 'D' and resid 404 through 457 removed outlier: 4.027A pdb=" N GLN D 455 " --> pdb=" O LYS D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 488 through 503 removed outlier: 3.827A pdb=" N TYR D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU D 494 " --> pdb=" O PRO D 490 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU D 495 " --> pdb=" O LYS D 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'E' and resid 568 through 571 Processing helix chain 'F' and resid 653 through 655 No H-bonds generated for 'chain 'F' and resid 653 through 655' Processing helix chain 'F' and resid 703 through 707 Processing helix chain 'G' and resid 60 through 67 Processing helix chain 'G' and resid 68 through 75 removed outlier: 3.898A pdb=" N GLU G 72 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU G 73 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 122 through 127 removed outlier: 4.340A pdb=" N TRP G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 195 Processing helix chain 'I' and resid 367 through 389 Processing helix chain 'I' and resid 404 through 457 removed outlier: 4.027A pdb=" N GLN I 455 " --> pdb=" O LYS I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 Processing helix chain 'I' and resid 488 through 503 removed outlier: 3.827A pdb=" N TYR I 492 " --> pdb=" O ASP I 488 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU I 494 " --> pdb=" O PRO I 490 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU I 495 " --> pdb=" O LYS I 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 535 through 539 Processing helix chain 'J' and resid 568 through 571 Processing helix chain 'K' and resid 653 through 655 No H-bonds generated for 'chain 'K' and resid 653 through 655' Processing helix chain 'K' and resid 703 through 707 Processing sheet with id=AA1, first strand: chain 'B' and resid 361 through 366 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 48 removed outlier: 6.257A pdb=" N LEU A 45 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N CYS A 278 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.658A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER A 261 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A 115 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA A 259 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 117 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 257 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER A 261 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A 115 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA A 259 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 117 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 257 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.726A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289 removed outlier: 4.137A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 512 through 513 Processing sheet with id=AB4, first strand: chain 'H' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU H 517 " --> pdb=" O THR H 624 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE H 541 " --> pdb=" O ARG H 557 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG H 557 " --> pdb=" O PHE H 541 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 543 " --> pdb=" O MET H 555 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU H 517 " --> pdb=" O THR H 624 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 627 through 630 Processing sheet with id=AB7, first strand: chain 'L' and resid 633 through 636 removed outlier: 6.707A pdb=" N LEU L 657 " --> pdb=" O TYR L 673 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR L 673 " --> pdb=" O LEU L 657 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP L 659 " --> pdb=" O LEU L 671 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 633 through 636 Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 366 Processing sheet with id=AC1, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.256A pdb=" N LEU C 45 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N CYS C 278 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.660A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER C 261 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 115 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA C 259 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 117 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 257 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER C 261 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 115 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA C 259 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 117 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 257 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.725A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD1, first strand: chain 'C' and resid 287 through 289 removed outlier: 4.136A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 512 through 513 Processing sheet with id=AD3, first strand: chain 'E' and resid 517 through 518 removed outlier: 6.655A pdb=" N GLU E 517 " --> pdb=" O THR E 624 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE E 541 " --> pdb=" O ARG E 557 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG E 557 " --> pdb=" O PHE E 541 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP E 543 " --> pdb=" O MET E 555 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 517 through 518 removed outlier: 6.655A pdb=" N GLU E 517 " --> pdb=" O THR E 624 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 627 through 630 Processing sheet with id=AD6, first strand: chain 'F' and resid 633 through 636 removed outlier: 6.707A pdb=" N LEU F 657 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR F 673 " --> pdb=" O LEU F 657 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP F 659 " --> pdb=" O LEU F 671 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 633 through 636 Processing sheet with id=AD8, first strand: chain 'I' and resid 361 through 366 Processing sheet with id=AD9, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AE1, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AE2, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AE3, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.256A pdb=" N LEU G 45 " --> pdb=" O ASP G 276 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N CYS G 278 " --> pdb=" O LEU G 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.659A pdb=" N LEU G 54 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER G 261 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 115 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA G 259 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG G 117 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA G 257 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 112 through 119 removed outlier: 7.198A pdb=" N SER G 261 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 115 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA G 259 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG G 117 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA G 257 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 136 through 141 removed outlier: 4.726A pdb=" N CYS G 139 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER G 146 " --> pdb=" O CYS G 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE9, first strand: chain 'G' and resid 287 through 289 removed outlier: 4.136A pdb=" N CYS G 282 " --> pdb=" O ILE G 289 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 512 through 513 Processing sheet with id=AF2, first strand: chain 'J' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU J 517 " --> pdb=" O THR J 624 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE J 541 " --> pdb=" O ARG J 557 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG J 557 " --> pdb=" O PHE J 541 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP J 543 " --> pdb=" O MET J 555 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 517 through 518 removed outlier: 6.656A pdb=" N GLU J 517 " --> pdb=" O THR J 624 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 627 through 630 Processing sheet with id=AF5, first strand: chain 'K' and resid 633 through 636 removed outlier: 6.707A pdb=" N LEU K 657 " --> pdb=" O TYR K 673 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR K 673 " --> pdb=" O LEU K 657 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP K 659 " --> pdb=" O LEU K 671 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 633 through 636 741 hydrogen bonds defined for protein. 1926 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: 6.85 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5141 1.33 - 1.48: 5396 1.48 - 1.62: 6887 1.62 - 1.76: 36 1.76 - 1.90: 93 Bond restraints: 17553 Sorted by residual: bond pdb=" CB ILE I 503 " pdb=" CG1 ILE I 503 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" CB ILE D 503 " pdb=" CG1 ILE D 503 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CB ILE B 503 " pdb=" CG1 ILE B 503 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" CB ILE B 336 " pdb=" CG1 ILE B 336 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CB ILE D 336 " pdb=" CG1 ILE D 336 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 17548 not shown) Histogram of bond angle deviations from ideal: 90.54 - 104.11: 273 104.11 - 117.67: 12655 117.67 - 131.23: 10825 131.23 - 144.79: 67 144.79 - 158.35: 3 Bond angle restraints: 23823 Sorted by residual: angle pdb=" N TYR H 609 " pdb=" CA TYR H 609 " pdb=" C TYR H 609 " ideal model delta sigma weight residual 113.12 90.54 22.58 1.25e+00 6.40e-01 3.26e+02 angle pdb=" N TYR E 609 " pdb=" CA TYR E 609 " pdb=" C TYR E 609 " ideal model delta sigma weight residual 113.12 90.57 22.55 1.25e+00 6.40e-01 3.25e+02 angle pdb=" N TYR J 609 " pdb=" CA TYR J 609 " pdb=" C TYR J 609 " ideal model delta sigma weight residual 113.12 90.58 22.54 1.25e+00 6.40e-01 3.25e+02 angle pdb=" C2 NAG G 404 " pdb=" N2 NAG G 404 " pdb=" C7 NAG G 404 " ideal model delta sigma weight residual 124.56 158.35 -33.79 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C2 NAG C 404 " pdb=" N2 NAG C 404 " pdb=" C7 NAG C 404 " ideal model delta sigma weight residual 124.56 158.32 -33.76 3.00e+00 1.11e-01 1.27e+02 ... (remaining 23818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 9931 17.16 - 34.32: 254 34.32 - 51.48: 63 51.48 - 68.64: 46 68.64 - 85.80: 17 Dihedral angle restraints: 10311 sinusoidal: 4119 harmonic: 6192 Sorted by residual: dihedral pdb=" CB CYS D 474 " pdb=" SG CYS D 474 " pdb=" SG CYS D 478 " pdb=" CB CYS D 478 " ideal model delta sinusoidal sigma weight residual 93.00 146.18 -53.18 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CB CYS B 474 " pdb=" SG CYS B 474 " pdb=" SG CYS B 478 " pdb=" CB CYS B 478 " ideal model delta sinusoidal sigma weight residual 93.00 146.15 -53.15 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CB CYS I 474 " pdb=" SG CYS I 474 " pdb=" SG CYS I 478 " pdb=" CB CYS I 478 " ideal model delta sinusoidal sigma weight residual 93.00 146.14 -53.14 1 1.00e+01 1.00e-02 3.84e+01 ... (remaining 10308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1883 0.100 - 0.199: 555 0.199 - 0.299: 111 0.299 - 0.398: 32 0.398 - 0.498: 26 Chirality restraints: 2607 Sorted by residual: chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 3.14 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CB ILE D 336 " pdb=" CA ILE D 336 " pdb=" CG1 ILE D 336 " pdb=" CG2 ILE D 336 " both_signs ideal model delta sigma weight residual False 2.64 3.14 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CB ILE I 336 " pdb=" CA ILE I 336 " pdb=" CG1 ILE I 336 " pdb=" CG2 ILE I 336 " both_signs ideal model delta sigma weight residual False 2.64 3.14 -0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 2604 not shown) Planarity restraints: 3078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 449 " 0.063 2.00e-02 2.50e+03 3.46e-02 2.39e+01 pdb=" CG TYR D 449 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 449 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR D 449 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 449 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR D 449 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR D 449 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 449 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 449 " -0.062 2.00e-02 2.50e+03 3.44e-02 2.36e+01 pdb=" CG TYR B 449 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 449 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 449 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 449 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR B 449 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR B 449 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 449 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 449 " -0.062 2.00e-02 2.50e+03 3.44e-02 2.36e+01 pdb=" CG TYR I 449 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR I 449 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR I 449 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR I 449 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR I 449 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR I 449 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 449 " -0.053 2.00e-02 2.50e+03 ... (remaining 3075 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 3 1.89 - 2.64: 321 2.64 - 3.40: 21609 3.40 - 4.15: 44659 4.15 - 4.90: 76626 Nonbonded interactions: 143218 Sorted by model distance: nonbonded pdb=" NE2 GLN L 714 " pdb=" CG2 THR L 721 " model vdw 1.142 3.540 nonbonded pdb=" CD1 LEU L 627 " pdb=" OE1 GLN L 714 " model vdw 1.750 3.460 nonbonded pdb=" CD GLN L 714 " pdb=" CG2 THR L 721 " model vdw 1.786 3.690 nonbonded pdb=" NE2 GLN B 372 " pdb=" OG SER H 607 " model vdw 2.099 2.520 nonbonded pdb=" N TYR E 609 " pdb=" N PHE E 610 " model vdw 2.215 2.560 ... (remaining 143213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.660 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 45.890 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.022 0.166 17553 Z= 1.417 Angle : 1.786 33.790 23823 Z= 1.182 Chirality : 0.109 0.498 2607 Planarity : 0.009 0.055 3063 Dihedral : 10.470 85.803 6291 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2121 helix: 1.24 (0.24), residues: 363 sheet: 1.19 (0.23), residues: 504 loop : 0.65 (0.17), residues: 1254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 422 time to evaluate : 1.830 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 425 average time/residue: 0.3424 time to fit residues: 209.0837 Evaluate side-chains 231 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 1.984 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1911 time to fit residues: 3.7082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 296 GLN C 55 GLN C 296 GLN E 540 GLN G 55 GLN G 296 GLN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17553 Z= 0.225 Angle : 0.609 8.603 23823 Z= 0.334 Chirality : 0.046 0.222 2607 Planarity : 0.004 0.033 3063 Dihedral : 6.021 81.697 2340 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.18), residues: 2121 helix: 2.31 (0.25), residues: 369 sheet: 0.66 (0.20), residues: 642 loop : 0.53 (0.19), residues: 1110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 269 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 290 average time/residue: 0.3073 time to fit residues: 135.4219 Evaluate side-chains 252 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 231 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1849 time to fit residues: 9.5719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 203 optimal weight: 0.2980 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17553 Z= 0.223 Angle : 0.555 9.552 23823 Z= 0.298 Chirality : 0.045 0.258 2607 Planarity : 0.004 0.036 3063 Dihedral : 5.767 80.124 2340 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2121 helix: 2.52 (0.26), residues: 369 sheet: 0.62 (0.20), residues: 627 loop : 0.39 (0.18), residues: 1125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 256 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 266 average time/residue: 0.3070 time to fit residues: 122.9443 Evaluate side-chains 241 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 227 time to evaluate : 2.069 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.1927 time to fit residues: 7.6590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 89 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 98 optimal weight: 0.0970 chunk 179 optimal weight: 3.9990 chunk 53 optimal weight: 0.0670 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 17553 Z= 0.135 Angle : 0.509 8.633 23823 Z= 0.272 Chirality : 0.043 0.204 2607 Planarity : 0.004 0.043 3063 Dihedral : 5.502 81.857 2340 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2121 helix: 2.86 (0.26), residues: 372 sheet: 0.51 (0.21), residues: 615 loop : 0.42 (0.18), residues: 1134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 258 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 262 average time/residue: 0.3004 time to fit residues: 118.7966 Evaluate side-chains 247 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 236 time to evaluate : 1.947 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2003 time to fit residues: 6.6198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN C 231 ASN D 372 GLN G 231 ASN ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 372 GLN ** K 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.089 17553 Z= 0.582 Angle : 0.757 10.712 23823 Z= 0.390 Chirality : 0.055 0.599 2607 Planarity : 0.006 0.055 3063 Dihedral : 6.219 80.041 2340 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2121 helix: 2.22 (0.26), residues: 366 sheet: 0.36 (0.21), residues: 579 loop : -0.18 (0.18), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 247 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 261 average time/residue: 0.3208 time to fit residues: 124.8998 Evaluate side-chains 257 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 233 time to evaluate : 2.060 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.1795 time to fit residues: 10.4875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS C 41 HIS C 248 ASN D 356 HIS G 41 HIS I 355 HIS K 713 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 17553 Z= 0.214 Angle : 0.540 9.779 23823 Z= 0.285 Chirality : 0.045 0.520 2607 Planarity : 0.004 0.040 3063 Dihedral : 5.704 81.433 2340 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2121 helix: 2.67 (0.26), residues: 369 sheet: 0.36 (0.21), residues: 582 loop : -0.04 (0.18), residues: 1170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 252 average time/residue: 0.3024 time to fit residues: 115.7195 Evaluate side-chains 240 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 230 time to evaluate : 2.037 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1693 time to fit residues: 5.9130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 17553 Z= 0.229 Angle : 0.549 9.458 23823 Z= 0.288 Chirality : 0.045 0.445 2607 Planarity : 0.004 0.040 3063 Dihedral : 5.613 80.558 2340 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2121 helix: 2.80 (0.26), residues: 369 sheet: 0.35 (0.21), residues: 612 loop : 0.00 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 234 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 239 average time/residue: 0.3046 time to fit residues: 111.8828 Evaluate side-chains 237 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 227 time to evaluate : 1.965 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1681 time to fit residues: 5.8549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 126 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 98 optimal weight: 0.0370 chunk 18 optimal weight: 0.0770 chunk 156 optimal weight: 0.6980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 HIS ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 17553 Z= 0.136 Angle : 0.490 9.641 23823 Z= 0.259 Chirality : 0.043 0.380 2607 Planarity : 0.004 0.034 3063 Dihedral : 5.281 80.995 2340 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2121 helix: 3.05 (0.26), residues: 375 sheet: 0.44 (0.21), residues: 612 loop : 0.17 (0.18), residues: 1134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 248 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 251 average time/residue: 0.3011 time to fit residues: 114.1642 Evaluate side-chains 236 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 232 time to evaluate : 1.879 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1603 time to fit residues: 3.8204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 17553 Z= 0.257 Angle : 0.570 10.256 23823 Z= 0.294 Chirality : 0.045 0.359 2607 Planarity : 0.004 0.037 3063 Dihedral : 5.489 80.765 2340 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.18), residues: 2121 helix: 2.89 (0.26), residues: 372 sheet: 0.46 (0.21), residues: 612 loop : 0.06 (0.18), residues: 1137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 232 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 236 average time/residue: 0.2978 time to fit residues: 107.8567 Evaluate side-chains 231 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 1.974 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1664 time to fit residues: 4.6094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 136 optimal weight: 0.0770 chunk 206 optimal weight: 0.0030 chunk 189 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.5948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 17553 Z= 0.173 Angle : 0.523 10.652 23823 Z= 0.271 Chirality : 0.044 0.346 2607 Planarity : 0.004 0.035 3063 Dihedral : 5.331 81.204 2340 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2121 helix: 3.00 (0.26), residues: 375 sheet: 0.50 (0.21), residues: 612 loop : 0.15 (0.19), residues: 1134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 231 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 233 average time/residue: 0.3178 time to fit residues: 113.1611 Evaluate side-chains 234 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 1.983 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1639 time to fit residues: 4.3036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135344 restraints weight = 20739.686| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.73 r_work: 0.3284 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 17553 Z= 0.201 Angle : 0.538 10.646 23823 Z= 0.277 Chirality : 0.044 0.334 2607 Planarity : 0.004 0.036 3063 Dihedral : 5.343 80.989 2340 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.18), residues: 2121 helix: 3.07 (0.26), residues: 372 sheet: 0.43 (0.21), residues: 618 loop : 0.15 (0.19), residues: 1131 =============================================================================== Job complete usr+sys time: 3659.62 seconds wall clock time: 67 minutes 35.44 seconds (4055.44 seconds total)