Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 04:52:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nii_12360/08_2023/7nii_12360_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nii_12360/08_2023/7nii_12360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nii_12360/08_2023/7nii_12360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nii_12360/08_2023/7nii_12360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nii_12360/08_2023/7nii_12360_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nii_12360/08_2023/7nii_12360_updated.pdb" } resolution = 2.88 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= 0.006 sd= 0.079 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 113 5.16 5 C 23689 2.51 5 N 6345 2.21 5 O 7064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 64": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "B GLU 675": "OE1" <-> "OE2" Residue "C GLU 675": "OE1" <-> "OE2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 675": "OE1" <-> "OE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E GLU 675": "OE1" <-> "OE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F GLU 675": "OE1" <-> "OE2" Residue "G GLU 675": "OE1" <-> "OE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H GLU 675": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 37235 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "B" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4363 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Chain: "C" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4367 Classifications: {'peptide': 565} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 541} Chain breaks: 3 Chain: "D" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "E" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4050 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 3 Chain: "F" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "G" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4363 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Chain: "H" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4367 Classifications: {'peptide': 565} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 541} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.31, per 1000 atoms: 0.46 Number of scatterers: 37235 At special positions: 0 Unit cell: (160.826, 161.655, 172.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 113 16.00 P 16 15.00 Mg 8 11.99 O 7064 8.00 N 6345 7.00 C 23689 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: 13.93 Conformation dependent library (CDL) restraints added in 5.4 seconds 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8878 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 39 sheets defined 46.1% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.69 Creating SS restraints... Processing helix chain 'A' and resid 19 through 50 removed outlier: 5.397A pdb=" N LYS A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.762A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 241 through 265 removed outlier: 3.829A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 306 through 335 removed outlier: 3.521A pdb=" N GLN A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 365 Processing helix chain 'A' and resid 369 through 403 removed outlier: 3.946A pdb=" N VAL A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 451 Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 497 through 500 No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 505 through 520 removed outlier: 3.631A pdb=" N PHE A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 552 Processing helix chain 'A' and resid 570 through 574 Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 592 through 595 No H-bonds generated for 'chain 'A' and resid 592 through 595' Processing helix chain 'A' and resid 616 through 619 No H-bonds generated for 'chain 'A' and resid 616 through 619' Processing helix chain 'A' and resid 623 through 635 removed outlier: 3.924A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 removed outlier: 3.996A pdb=" N ARG A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 686 removed outlier: 3.514A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'B' and resid 19 through 50 removed outlier: 5.398A pdb=" N LYS B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 96 through 106 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 241 through 277 removed outlier: 3.829A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 404 removed outlier: 3.525A pdb=" N ALA B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 451 Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 497 through 500 No H-bonds generated for 'chain 'B' and resid 497 through 500' Processing helix chain 'B' and resid 505 through 520 removed outlier: 3.631A pdb=" N PHE B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 552 Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 582 through 586 Processing helix chain 'B' and resid 592 through 595 No H-bonds generated for 'chain 'B' and resid 592 through 595' Processing helix chain 'B' and resid 616 through 619 No H-bonds generated for 'chain 'B' and resid 616 through 619' Processing helix chain 'B' and resid 623 through 635 removed outlier: 3.925A pdb=" N GLN B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 657 removed outlier: 3.997A pdb=" N ARG B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 686 removed outlier: 3.513A pdb=" N SER B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'C' and resid 19 through 50 removed outlier: 5.398A pdb=" N LYS C 31 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 93 removed outlier: 3.763A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 241 through 277 removed outlier: 3.829A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 404 Processing helix chain 'C' and resid 426 through 451 Processing helix chain 'C' and resid 458 through 463 Processing helix chain 'C' and resid 497 through 500 No H-bonds generated for 'chain 'C' and resid 497 through 500' Processing helix chain 'C' and resid 505 through 520 removed outlier: 3.632A pdb=" N PHE C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 552 Processing helix chain 'C' and resid 570 through 574 Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 592 through 595 No H-bonds generated for 'chain 'C' and resid 592 through 595' Processing helix chain 'C' and resid 616 through 619 No H-bonds generated for 'chain 'C' and resid 616 through 619' Processing helix chain 'C' and resid 623 through 635 removed outlier: 3.924A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 657 removed outlier: 3.998A pdb=" N ARG C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 686 removed outlier: 3.514A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'D' and resid 19 through 50 removed outlier: 5.397A pdb=" N LYS D 31 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.761A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 241 through 266 removed outlier: 3.831A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 306 through 335 removed outlier: 3.521A pdb=" N GLN D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 365 Processing helix chain 'D' and resid 369 through 403 removed outlier: 3.947A pdb=" N VAL D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 403 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 451 Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 497 through 500 No H-bonds generated for 'chain 'D' and resid 497 through 500' Processing helix chain 'D' and resid 505 through 520 removed outlier: 3.630A pdb=" N PHE D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 552 Processing helix chain 'D' and resid 570 through 574 Processing helix chain 'D' and resid 582 through 586 Processing helix chain 'D' and resid 592 through 595 No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 616 through 619 No H-bonds generated for 'chain 'D' and resid 616 through 619' Processing helix chain 'D' and resid 623 through 635 removed outlier: 3.923A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 657 removed outlier: 3.997A pdb=" N ARG D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 686 removed outlier: 3.515A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 707 Processing helix chain 'E' and resid 19 through 50 removed outlier: 5.397A pdb=" N LYS E 31 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU E 32 " --> pdb=" O ASP E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 93 removed outlier: 3.762A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 106 Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 209 through 219 Processing helix chain 'E' and resid 241 through 259 removed outlier: 3.831A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 451 Processing helix chain 'E' and resid 458 through 463 Processing helix chain 'E' and resid 497 through 500 No H-bonds generated for 'chain 'E' and resid 497 through 500' Processing helix chain 'E' and resid 505 through 520 removed outlier: 3.630A pdb=" N PHE E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 552 Processing helix chain 'E' and resid 570 through 574 Processing helix chain 'E' and resid 582 through 586 Processing helix chain 'E' and resid 592 through 595 No H-bonds generated for 'chain 'E' and resid 592 through 595' Processing helix chain 'E' and resid 616 through 619 No H-bonds generated for 'chain 'E' and resid 616 through 619' Processing helix chain 'E' and resid 623 through 635 removed outlier: 3.925A pdb=" N GLN E 634 " --> pdb=" O ASN E 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 651 through 657 removed outlier: 3.996A pdb=" N ARG E 657 " --> pdb=" O ALA E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 686 removed outlier: 3.514A pdb=" N SER E 686 " --> pdb=" O ARG E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 707 Processing helix chain 'F' and resid 19 through 50 removed outlier: 5.397A pdb=" N LYS F 31 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU F 32 " --> pdb=" O ASP F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 93 removed outlier: 3.761A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 209 through 219 Processing helix chain 'F' and resid 241 through 265 removed outlier: 3.830A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F 255 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN F 263 " --> pdb=" O ASN F 259 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 279 - end of helix Processing helix chain 'F' and resid 306 through 335 removed outlier: 3.522A pdb=" N GLN F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 365 Processing helix chain 'F' and resid 369 through 403 removed outlier: 3.946A pdb=" N VAL F 374 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE F 400 " --> pdb=" O GLN F 396 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 402 " --> pdb=" O LEU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 451 Processing helix chain 'F' and resid 458 through 463 Processing helix chain 'F' and resid 497 through 500 No H-bonds generated for 'chain 'F' and resid 497 through 500' Processing helix chain 'F' and resid 505 through 520 removed outlier: 3.631A pdb=" N PHE F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 552 Processing helix chain 'F' and resid 570 through 574 Processing helix chain 'F' and resid 582 through 586 Processing helix chain 'F' and resid 592 through 595 No H-bonds generated for 'chain 'F' and resid 592 through 595' Processing helix chain 'F' and resid 616 through 619 No H-bonds generated for 'chain 'F' and resid 616 through 619' Processing helix chain 'F' and resid 623 through 635 removed outlier: 3.926A pdb=" N GLN F 634 " --> pdb=" O ASN F 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 657 removed outlier: 3.997A pdb=" N ARG F 657 " --> pdb=" O ALA F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 686 removed outlier: 3.515A pdb=" N SER F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 707 Processing helix chain 'G' and resid 19 through 50 removed outlier: 5.396A pdb=" N LYS G 31 " --> pdb=" O ILE G 27 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU G 32 " --> pdb=" O ASP G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 93 removed outlier: 3.762A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 106 Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 209 through 219 Processing helix chain 'G' and resid 241 through 277 removed outlier: 3.829A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN G 263 " --> pdb=" O ASN G 259 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN G 266 " --> pdb=" O ARG G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 403 removed outlier: 3.928A pdb=" N SER G 403 " --> pdb=" O ASN G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 451 Processing helix chain 'G' and resid 458 through 463 Processing helix chain 'G' and resid 497 through 500 No H-bonds generated for 'chain 'G' and resid 497 through 500' Processing helix chain 'G' and resid 505 through 520 removed outlier: 3.630A pdb=" N PHE G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 552 Processing helix chain 'G' and resid 570 through 574 Processing helix chain 'G' and resid 582 through 586 Processing helix chain 'G' and resid 592 through 595 No H-bonds generated for 'chain 'G' and resid 592 through 595' Processing helix chain 'G' and resid 616 through 619 No H-bonds generated for 'chain 'G' and resid 616 through 619' Processing helix chain 'G' and resid 623 through 635 removed outlier: 3.926A pdb=" N GLN G 634 " --> pdb=" O ASN G 630 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 651 through 657 removed outlier: 3.997A pdb=" N ARG G 657 " --> pdb=" O ALA G 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 673 through 686 removed outlier: 3.514A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 702 through 707 Processing helix chain 'H' and resid 19 through 50 removed outlier: 5.398A pdb=" N LYS H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU H 32 " --> pdb=" O ASP H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 93 removed outlier: 3.762A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 106 Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 209 through 219 Processing helix chain 'H' and resid 241 through 277 removed outlier: 3.829A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN H 263 " --> pdb=" O ASN H 259 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN H 266 " --> pdb=" O ARG H 262 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP H 267 " --> pdb=" O GLN H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 404 removed outlier: 3.509A pdb=" N ALA H 401 " --> pdb=" O GLU H 397 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER H 403 " --> pdb=" O ASN H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 451 Processing helix chain 'H' and resid 458 through 463 Processing helix chain 'H' and resid 497 through 500 No H-bonds generated for 'chain 'H' and resid 497 through 500' Processing helix chain 'H' and resid 505 through 520 removed outlier: 3.632A pdb=" N PHE H 519 " --> pdb=" O THR H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 552 Processing helix chain 'H' and resid 570 through 574 Processing helix chain 'H' and resid 582 through 586 Processing helix chain 'H' and resid 592 through 595 No H-bonds generated for 'chain 'H' and resid 592 through 595' Processing helix chain 'H' and resid 616 through 619 No H-bonds generated for 'chain 'H' and resid 616 through 619' Processing helix chain 'H' and resid 623 through 635 removed outlier: 3.924A pdb=" N GLN H 634 " --> pdb=" O ASN H 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN H 635 " --> pdb=" O TRP H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 657 removed outlier: 3.996A pdb=" N ARG H 657 " --> pdb=" O ALA H 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 673 through 686 removed outlier: 3.513A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 702 through 707 Processing sheet with id= A, first strand: chain 'A' and resid 416 through 418 removed outlier: 3.589A pdb=" N VAL A 416 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU A 56 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 110 through 114 Processing sheet with id= C, first strand: chain 'A' and resid 182 through 184 removed outlier: 3.827A pdb=" N ARG A 139 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN A 192 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE A 137 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 468 through 472 removed outlier: 7.969A pdb=" N CYS A 693 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER A 471 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 695 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A 692 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 639 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE A 531 " --> pdb=" O ILE A 639 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 641 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLY A 533 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP A 605 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP A 562 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE A 607 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 60 through 62 removed outlier: 4.193A pdb=" N LEU A 60 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 413 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLN A 62 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 411 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 416 through 418 removed outlier: 3.590A pdb=" N VAL B 416 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU B 56 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 110 through 114 Processing sheet with id= H, first strand: chain 'B' and resid 182 through 184 removed outlier: 3.826A pdb=" N ARG B 139 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN B 192 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE B 137 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 468 through 472 removed outlier: 7.969A pdb=" N CYS B 693 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER B 471 " --> pdb=" O CYS B 693 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 695 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B 692 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE B 639 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE B 531 " --> pdb=" O ILE B 639 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 641 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLY B 533 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP B 605 " --> pdb=" O PHE B 560 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP B 562 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 607 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 416 through 418 removed outlier: 3.589A pdb=" N VAL C 416 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU C 56 " --> pdb=" O ASP C 418 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 110 through 114 Processing sheet with id= L, first strand: chain 'C' and resid 182 through 184 removed outlier: 3.825A pdb=" N ARG C 139 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 192 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE C 137 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 468 through 472 removed outlier: 7.968A pdb=" N CYS C 693 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER C 471 " --> pdb=" O CYS C 693 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C 695 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 692 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE C 639 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE C 531 " --> pdb=" O ILE C 639 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE C 641 " --> pdb=" O ILE C 531 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLY C 533 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP C 605 " --> pdb=" O PHE C 560 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP C 562 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE C 607 " --> pdb=" O ASP C 562 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.783A pdb=" N GLN C 62 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE C 411 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 416 through 418 removed outlier: 3.589A pdb=" N VAL D 416 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU D 56 " --> pdb=" O ASP D 418 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 110 through 114 Processing sheet with id= Q, first strand: chain 'D' and resid 182 through 184 removed outlier: 3.826A pdb=" N ARG D 139 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN D 192 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE D 137 " --> pdb=" O ASN D 192 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 468 through 472 removed outlier: 7.968A pdb=" N CYS D 693 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER D 471 " --> pdb=" O CYS D 693 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU D 695 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY D 692 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 639 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE D 531 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE D 641 " --> pdb=" O ILE D 531 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLY D 533 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP D 605 " --> pdb=" O PHE D 560 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP D 562 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE D 607 " --> pdb=" O ASP D 562 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.496A pdb=" N GLN D 62 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE D 411 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 416 through 418 removed outlier: 3.589A pdb=" N VAL E 416 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU E 56 " --> pdb=" O ASP E 418 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 110 through 114 Processing sheet with id= V, first strand: chain 'E' and resid 182 through 184 removed outlier: 3.826A pdb=" N ARG E 139 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN E 192 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE E 137 " --> pdb=" O ASN E 192 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 468 through 472 removed outlier: 7.968A pdb=" N CYS E 693 " --> pdb=" O TYR E 469 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER E 471 " --> pdb=" O CYS E 693 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU E 695 " --> pdb=" O SER E 471 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY E 692 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE E 639 " --> pdb=" O LEU E 529 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE E 531 " --> pdb=" O ILE E 639 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE E 641 " --> pdb=" O ILE E 531 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY E 533 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP E 605 " --> pdb=" O PHE E 560 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP E 562 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE E 607 " --> pdb=" O ASP E 562 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.626A pdb=" N GLN E 62 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE E 411 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 416 through 418 removed outlier: 3.590A pdb=" N VAL F 416 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU F 56 " --> pdb=" O ASP F 418 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 110 through 114 Processing sheet with id= AA, first strand: chain 'F' and resid 182 through 184 removed outlier: 3.826A pdb=" N ARG F 139 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN F 192 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE F 137 " --> pdb=" O ASN F 192 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 468 through 472 removed outlier: 7.968A pdb=" N CYS F 693 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER F 471 " --> pdb=" O CYS F 693 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU F 695 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY F 692 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE F 639 " --> pdb=" O LEU F 529 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE F 531 " --> pdb=" O ILE F 639 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE F 641 " --> pdb=" O ILE F 531 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLY F 533 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP F 605 " --> pdb=" O PHE F 560 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP F 562 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE F 607 " --> pdb=" O ASP F 562 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 60 through 62 removed outlier: 7.002A pdb=" N GLN F 62 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE F 411 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 416 through 418 removed outlier: 3.590A pdb=" N VAL G 416 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU G 56 " --> pdb=" O ASP G 418 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 110 through 114 Processing sheet with id= AF, first strand: chain 'G' and resid 182 through 184 removed outlier: 3.826A pdb=" N ARG G 139 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN G 192 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE G 137 " --> pdb=" O ASN G 192 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 468 through 472 removed outlier: 7.969A pdb=" N CYS G 693 " --> pdb=" O TYR G 469 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER G 471 " --> pdb=" O CYS G 693 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU G 695 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY G 692 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE G 639 " --> pdb=" O LEU G 529 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE G 531 " --> pdb=" O ILE G 639 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE G 641 " --> pdb=" O ILE G 531 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N GLY G 533 " --> pdb=" O ILE G 641 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP G 605 " --> pdb=" O PHE G 560 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP G 562 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE G 607 " --> pdb=" O ASP G 562 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 60 through 63 removed outlier: 3.553A pdb=" N ASP G 413 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN G 62 " --> pdb=" O ILE G 411 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE G 411 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 416 through 418 removed outlier: 3.588A pdb=" N VAL H 416 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU H 56 " --> pdb=" O ASP H 418 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 110 through 114 Processing sheet with id= AK, first strand: chain 'H' and resid 182 through 184 removed outlier: 3.826A pdb=" N ARG H 139 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN H 192 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE H 137 " --> pdb=" O ASN H 192 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 468 through 472 removed outlier: 7.968A pdb=" N CYS H 693 " --> pdb=" O TYR H 469 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER H 471 " --> pdb=" O CYS H 693 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU H 695 " --> pdb=" O SER H 471 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY H 692 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE H 639 " --> pdb=" O LEU H 529 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE H 531 " --> pdb=" O ILE H 639 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE H 641 " --> pdb=" O ILE H 531 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLY H 533 " --> pdb=" O ILE H 641 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP H 605 " --> pdb=" O PHE H 560 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP H 562 " --> pdb=" O ASP H 605 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE H 607 " --> pdb=" O ASP H 562 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 60 through 62 removed outlier: 5.908A pdb=" N GLN H 62 " --> pdb=" O ILE H 411 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE H 411 " --> pdb=" O GLN H 62 " (cutoff:3.500A) 1857 hydrogen bonds defined for protein. 5457 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: 14.25 Time building geometry restraints manager: 14.97 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: 12263 1.34 - 1.46: 4449 1.46 - 1.57: 20851 1.57 - 1.69: 24 1.69 - 1.81: 210 Bond restraints: 37797 Sorted by residual: bond pdb=" C ASP B 58 " pdb=" N ALA B 59 " ideal model delta sigma weight residual 1.330 1.523 -0.194 1.41e-02 5.03e+03 1.88e+02 bond pdb=" C6 ADP C1000 " pdb=" N6 ADP C1000 " ideal model delta sigma weight residual 1.355 1.463 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C6 ADP H1000 " pdb=" N6 ADP H1000 " ideal model delta sigma weight residual 1.355 1.463 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C6 ADP B1000 " pdb=" N6 ADP B1000 " ideal model delta sigma weight residual 1.355 1.462 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C6 ADP G1000 " pdb=" N6 ADP G1000 " ideal model delta sigma weight residual 1.355 1.462 -0.107 2.00e-02 2.50e+03 2.87e+01 ... (remaining 37792 not shown) Histogram of bond angle deviations from ideal: 99.83 - 107.25: 1110 107.25 - 114.67: 23253 114.67 - 122.08: 20131 122.08 - 129.50: 6581 129.50 - 136.92: 133 Bond angle restraints: 51208 Sorted by residual: angle pdb=" N SER G 403 " pdb=" CA SER G 403 " pdb=" C SER G 403 " ideal model delta sigma weight residual 111.36 118.58 -7.22 1.09e+00 8.42e-01 4.38e+01 angle pdb=" C ASP B 58 " pdb=" N ALA B 59 " pdb=" CA ALA B 59 " ideal model delta sigma weight residual 122.81 112.65 10.16 1.68e+00 3.54e-01 3.66e+01 angle pdb=" N ASN B 408 " pdb=" CA ASN B 408 " pdb=" C ASN B 408 " ideal model delta sigma weight residual 111.28 104.73 6.55 1.09e+00 8.42e-01 3.61e+01 angle pdb=" N ALA D 265 " pdb=" CA ALA D 265 " pdb=" C ALA D 265 " ideal model delta sigma weight residual 111.28 117.09 -5.81 1.09e+00 8.42e-01 2.85e+01 angle pdb=" N GLY C 407 " pdb=" CA GLY C 407 " pdb=" C GLY C 407 " ideal model delta sigma weight residual 110.56 118.93 -8.37 1.66e+00 3.63e-01 2.54e+01 ... (remaining 51203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 22424 23.28 - 46.55: 566 46.55 - 69.83: 56 69.83 - 93.11: 32 93.11 - 116.39: 8 Dihedral angle restraints: 23086 sinusoidal: 9308 harmonic: 13778 Sorted by residual: dihedral pdb=" C5' ADP H1000 " pdb=" O5' ADP H1000 " pdb=" PA ADP H1000 " pdb=" O2A ADP H1000 " ideal model delta sinusoidal sigma weight residual -60.00 56.39 -116.39 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" C5' ADP G1000 " pdb=" O5' ADP G1000 " pdb=" PA ADP G1000 " pdb=" O2A ADP G1000 " ideal model delta sinusoidal sigma weight residual -60.00 56.28 -116.28 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" C5' ADP B1000 " pdb=" O5' ADP B1000 " pdb=" PA ADP B1000 " pdb=" O2A ADP B1000 " ideal model delta sinusoidal sigma weight residual -60.00 56.27 -116.27 1 2.00e+01 2.50e-03 3.46e+01 ... (remaining 23083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5227 0.058 - 0.115: 722 0.115 - 0.173: 99 0.173 - 0.230: 8 0.230 - 0.288: 4 Chirality restraints: 6060 Sorted by residual: chirality pdb=" CA ILE D 411 " pdb=" N ILE D 411 " pdb=" C ILE D 411 " pdb=" CB ILE D 411 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA VAL A 409 " pdb=" N VAL A 409 " pdb=" C VAL A 409 " pdb=" CB VAL A 409 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE F 411 " pdb=" N ILE F 411 " pdb=" C ILE F 411 " pdb=" CB ILE F 411 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 6057 not shown) Planarity restraints: 6517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 58 " 0.021 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" C ASP B 58 " -0.076 2.00e-02 2.50e+03 pdb=" O ASP B 58 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA B 59 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 402 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C LYS A 402 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS A 402 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 403 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 251 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.45e+00 pdb=" C ILE B 251 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE B 251 " -0.010 2.00e-02 2.50e+03 pdb=" N SER B 252 " -0.009 2.00e-02 2.50e+03 ... (remaining 6514 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.95: 21 1.95 - 2.69: 954 2.69 - 3.43: 53849 3.43 - 4.16: 92905 4.16 - 4.90: 165886 Nonbonded interactions: 313615 Sorted by model distance: nonbonded pdb=" CG GLU C 64 " pdb=" NH2 ARG C 410 " model vdw 1.216 3.520 nonbonded pdb=" OG SER B 403 " pdb=" CD1 PHE C 273 " model vdw 1.362 3.340 nonbonded pdb=" OE1 GLU H 64 " pdb=" O ASN H 408 " model vdw 1.441 3.040 nonbonded pdb=" OE2 GLU C 64 " pdb=" NH1 ARG C 410 " model vdw 1.509 2.520 nonbonded pdb=" N ILE G 63 " pdb=" O GLY G 230 " model vdw 1.610 2.520 ... (remaining 313610 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' and (resid 17 through 279 or resid 385 through 721 or resid 1000 thro \ ugh 1001)) selection = chain 'B' selection = (chain 'C' and (resid 17 through 279 or resid 385 through 721 or resid 1000 thro \ ugh 1001)) selection = (chain 'D' and (resid 17 through 279 or resid 385 through 721 or resid 1000 thro \ ugh 1001)) selection = (chain 'F' and (resid 17 through 279 or resid 385 through 721 or resid 1000 thro \ ugh 1001)) selection = chain 'G' selection = (chain 'H' and (resid 17 through 279 or resid 385 through 721 or resid 1000 thro \ ugh 1001)) } 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: 3.660 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: 0.040 Extract box with map and model: 14.160 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 89.460 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.006 0.194 37797 Z= 0.402 Angle : 0.692 11.195 51208 Z= 0.382 Chirality : 0.043 0.288 6060 Planarity : 0.003 0.044 6517 Dihedral : 11.054 116.386 14208 Min Nonbonded Distance : 1.216 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.10), residues: 4708 helix: -1.71 (0.09), residues: 2315 sheet: -0.85 (0.18), residues: 636 loop : -2.09 (0.12), residues: 1757 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 740 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 4 residues processed: 740 average time/residue: 1.2708 time to fit residues: 1161.8016 Evaluate side-chains 498 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 494 time to evaluate : 4.246 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 3 average time/residue: 0.5191 time to fit residues: 8.8640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 1.9990 chunk 359 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 242 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 chunk 371 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 430 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 111 GLN A 173 GLN ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 254 ASN A 275 ASN A 351 GLN A 518 HIS ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 HIS B 29 HIS B 111 GLN B 173 GLN B 254 ASN ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN B 395 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 HIS C 111 GLN C 254 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN C 571 HIS C 576 HIS D 111 GLN D 175 ASN D 254 ASN D 275 ASN D 571 HIS D 576 HIS E 29 HIS E 111 GLN E 173 GLN E 254 ASN E 518 HIS ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 576 HIS E 611 GLN E 671 ASN F 29 HIS F 111 GLN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 275 ASN F 317 ASN F 321 GLN F 399 ASN F 571 HIS F 576 HIS G 111 GLN G 173 GLN G 246 HIS G 254 ASN G 263 GLN G 277 GLN ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 576 HIS H 111 GLN H 168 ASN H 253 GLN H 277 GLN H 571 HIS H 576 HIS Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 37797 Z= 0.231 Angle : 0.614 7.976 51208 Z= 0.298 Chirality : 0.044 0.191 6060 Planarity : 0.004 0.030 6517 Dihedral : 5.398 62.105 5198 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: -0.82 (0.11), residues: 4708 helix: 0.19 (0.10), residues: 2353 sheet: -0.32 (0.17), residues: 646 loop : -1.58 (0.13), residues: 1709 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 545 time to evaluate : 4.152 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 outliers start: 113 outliers final: 23 residues processed: 604 average time/residue: 1.2334 time to fit residues: 935.0921 Evaluate side-chains 484 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 461 time to evaluate : 4.181 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 14 residues processed: 11 average time/residue: 0.6719 time to fit residues: 17.0232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 358 optimal weight: 0.8980 chunk 293 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 431 optimal weight: 4.9990 chunk 465 optimal weight: 1.9990 chunk 384 optimal weight: 2.9990 chunk 427 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 345 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 321 GLN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 ASN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN G 571 HIS H 253 GLN ** H 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 37797 Z= 0.247 Angle : 0.603 10.327 51208 Z= 0.289 Chirality : 0.044 0.172 6060 Planarity : 0.003 0.037 6517 Dihedral : 5.451 63.162 5198 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.45 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: -0.08 (0.12), residues: 4708 helix: 0.96 (0.10), residues: 2357 sheet: -0.14 (0.18), residues: 604 loop : -1.39 (0.13), residues: 1747 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 487 time to evaluate : 4.129 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: 132 outliers final: 44 residues processed: 558 average time/residue: 1.2823 time to fit residues: 893.6696 Evaluate side-chains 486 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 442 time to evaluate : 4.078 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 28 residues processed: 20 average time/residue: 0.3974 time to fit residues: 19.3954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 9.9990 chunk 324 optimal weight: 8.9990 chunk 223 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 289 optimal weight: 0.0370 chunk 432 optimal weight: 0.0060 chunk 458 optimal weight: 0.9980 chunk 226 optimal weight: 0.6980 chunk 410 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 0.5074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS B 259 ASN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 399 ASN D 183 ASN D 399 ASN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 GLN H 258 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 37797 Z= 0.147 Angle : 0.564 10.385 51208 Z= 0.266 Chirality : 0.042 0.177 6060 Planarity : 0.003 0.030 6517 Dihedral : 4.925 54.047 5198 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.50 (0.12), residues: 4708 helix: 1.51 (0.11), residues: 2341 sheet: 0.16 (0.19), residues: 608 loop : -1.23 (0.13), residues: 1759 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 505 time to evaluate : 4.098 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 outliers start: 105 outliers final: 35 residues processed: 566 average time/residue: 1.2574 time to fit residues: 890.1343 Evaluate side-chains 488 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 453 time to evaluate : 4.217 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 23 residues processed: 14 average time/residue: 0.5232 time to fit residues: 17.4118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 7.9990 chunk 260 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 341 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 390 optimal weight: 1.9990 chunk 316 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 0.4980 chunk 411 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 37797 Z= 0.191 Angle : 0.580 10.766 51208 Z= 0.273 Chirality : 0.043 0.163 6060 Planarity : 0.003 0.030 6517 Dihedral : 5.024 54.485 5198 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.71 (0.12), residues: 4708 helix: 1.72 (0.11), residues: 2340 sheet: 0.26 (0.19), residues: 612 loop : -1.18 (0.13), residues: 1756 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 478 time to evaluate : 4.293 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 outliers start: 97 outliers final: 45 residues processed: 534 average time/residue: 1.2258 time to fit residues: 822.8437 Evaluate side-chains 497 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 452 time to evaluate : 4.173 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 29 residues processed: 20 average time/residue: 0.4924 time to fit residues: 21.6265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 2.9990 chunk 412 optimal weight: 5.9990 chunk 90 optimal weight: 50.0000 chunk 269 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 458 optimal weight: 0.9990 chunk 380 optimal weight: 0.5980 chunk 212 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN B 114 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 ASN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 ASN H 168 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 37797 Z= 0.190 Angle : 0.587 10.802 51208 Z= 0.275 Chirality : 0.043 0.157 6060 Planarity : 0.003 0.030 6517 Dihedral : 5.042 55.473 5198 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.86 (0.12), residues: 4708 helix: 1.85 (0.11), residues: 2328 sheet: 0.36 (0.19), residues: 606 loop : -1.12 (0.13), residues: 1774 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 480 time to evaluate : 4.125 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 outliers start: 96 outliers final: 46 residues processed: 546 average time/residue: 1.2200 time to fit residues: 840.5038 Evaluate side-chains 497 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 451 time to evaluate : 4.282 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 37 residues processed: 13 average time/residue: 0.5253 time to fit residues: 16.9107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 6.9990 chunk 51 optimal weight: 0.0870 chunk 261 optimal weight: 2.9990 chunk 334 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 386 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 456 optimal weight: 0.5980 chunk 285 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 210 optimal weight: 40.0000 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 ASN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 266 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 37797 Z= 0.273 Angle : 0.624 10.995 51208 Z= 0.294 Chirality : 0.044 0.156 6060 Planarity : 0.003 0.037 6517 Dihedral : 5.457 63.301 5198 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.77 (0.12), residues: 4708 helix: 1.75 (0.11), residues: 2326 sheet: 0.29 (0.19), residues: 614 loop : -1.09 (0.14), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 468 time to evaluate : 4.022 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 outliers start: 104 outliers final: 55 residues processed: 530 average time/residue: 1.2199 time to fit residues: 817.3201 Evaluate side-chains 500 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 445 time to evaluate : 4.315 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 40 residues processed: 19 average time/residue: 0.4435 time to fit residues: 20.2713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 137 optimal weight: 0.1980 chunk 89 optimal weight: 30.0000 chunk 88 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 359 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN H 254 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 37797 Z= 0.334 Angle : 0.662 13.405 51208 Z= 0.314 Chirality : 0.046 0.219 6060 Planarity : 0.004 0.051 6517 Dihedral : 5.703 68.399 5198 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.65 (0.12), residues: 4708 helix: 1.61 (0.11), residues: 2330 sheet: 0.39 (0.19), residues: 611 loop : -1.16 (0.14), residues: 1767 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 465 time to evaluate : 4.168 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 outliers start: 102 outliers final: 60 residues processed: 524 average time/residue: 1.2066 time to fit residues: 796.5675 Evaluate side-chains 504 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 444 time to evaluate : 3.942 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 42 residues processed: 23 average time/residue: 0.5850 time to fit residues: 26.0083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 1.9990 chunk 437 optimal weight: 8.9990 chunk 399 optimal weight: 0.9990 chunk 425 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 185 optimal weight: 0.0670 chunk 334 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 384 optimal weight: 7.9990 chunk 402 optimal weight: 0.9990 chunk 424 optimal weight: 5.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 37797 Z= 0.241 Angle : 0.640 11.485 51208 Z= 0.302 Chirality : 0.044 0.218 6060 Planarity : 0.004 0.058 6517 Dihedral : 5.421 61.713 5198 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.52 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.75 (0.12), residues: 4708 helix: 1.71 (0.11), residues: 2327 sheet: 0.35 (0.19), residues: 612 loop : -1.11 (0.14), residues: 1769 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 460 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 45 residues processed: 515 average time/residue: 1.1960 time to fit residues: 782.4461 Evaluate side-chains 494 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 449 time to evaluate : 4.485 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 36 residues processed: 12 average time/residue: 0.5116 time to fit residues: 16.1695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 0.5980 chunk 450 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 213 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 chunk 472 optimal weight: 0.0870 chunk 434 optimal weight: 1.9990 chunk 376 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 317 ASN E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 37797 Z= 0.177 Angle : 0.623 11.474 51208 Z= 0.293 Chirality : 0.043 0.231 6060 Planarity : 0.003 0.050 6517 Dihedral : 5.056 55.239 5198 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.96 (0.12), residues: 4708 helix: 1.89 (0.11), residues: 2323 sheet: 0.49 (0.20), residues: 609 loop : -1.02 (0.14), residues: 1776 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 469 time to evaluate : 4.052 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: 51 outliers final: 40 residues processed: 507 average time/residue: 1.2155 time to fit residues: 787.7387 Evaluate side-chains 487 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 447 time to evaluate : 4.352 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 34 residues processed: 8 average time/residue: 0.4446 time to fit residues: 12.3561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 1.9990 chunk 400 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 346 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 376 optimal weight: 0.0470 chunk 157 optimal weight: 0.7980 chunk 386 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125260 restraints weight = 45637.464| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.98 r_work: 0.3124 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 37797 Z= 0.175 Angle : 0.621 11.555 51208 Z= 0.292 Chirality : 0.043 0.215 6060 Planarity : 0.003 0.048 6517 Dihedral : 4.972 55.301 5198 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.52 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.05 (0.12), residues: 4708 helix: 1.97 (0.11), residues: 2323 sheet: 0.52 (0.20), residues: 611 loop : -0.98 (0.14), residues: 1774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13653.35 seconds wall clock time: 243 minutes 11.79 seconds (14591.79 seconds total)