Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 14:50:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/04_2023/6q2r_20578_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/04_2023/6q2r_20578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/04_2023/6q2r_20578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/04_2023/6q2r_20578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/04_2023/6q2r_20578_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/04_2023/6q2r_20578_neut.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 16 9.91 5 S 276 5.16 5 C 18868 2.51 5 N 5476 2.21 5 O 5756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "C TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 205": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 415": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "D TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 415": "NH1" <-> "NH2" Residue "U ARG 106": "NH1" <-> "NH2" Residue "U ARG 151": "NH1" <-> "NH2" Residue "U ARG 153": "NH1" <-> "NH2" Residue "U ARG 155": "NH1" <-> "NH2" Residue "U ARG 158": "NH1" <-> "NH2" Residue "U ARG 182": "NH1" <-> "NH2" Residue "V ARG 106": "NH1" <-> "NH2" Residue "V ARG 151": "NH1" <-> "NH2" Residue "V ARG 153": "NH1" <-> "NH2" Residue "V ARG 155": "NH1" <-> "NH2" Residue "V ARG 158": "NH1" <-> "NH2" Residue "V ARG 182": "NH1" <-> "NH2" Residue "W ARG 42": "NH1" <-> "NH2" Residue "W ARG 58": "NH1" <-> "NH2" Residue "W ARG 97": "NH1" <-> "NH2" Residue "W TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 187": "NH1" <-> "NH2" Residue "W ARG 205": "NH1" <-> "NH2" Residue "Y ARG 67": "NH1" <-> "NH2" Residue "Y ARG 112": "NH1" <-> "NH2" Residue "Y ARG 415": "NH1" <-> "NH2" Residue "X ARG 42": "NH1" <-> "NH2" Residue "X ARG 58": "NH1" <-> "NH2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 187": "NH1" <-> "NH2" Residue "X ARG 205": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 112": "NH1" <-> "NH2" Residue "Z ARG 415": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 30392 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "C" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "E" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "D" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "F" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "U" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "V" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "W" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "Y" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "X" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "Z" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 16.55, per 1000 atoms: 0.54 Number of scatterers: 30392 At special positions: 0 Unit cell: (227.91, 222.56, 121.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 16 19.99 S 276 16.00 O 5756 8.00 N 5476 7.00 C 18868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=106, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS B 164 " distance=1.96 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 93 " distance=2.04 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 222 " distance=2.02 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 174 " distance=2.02 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 200 " distance=2.02 Simple disulfide: pdb=" SG CYS C 195 " - pdb=" SG CYS C 241 " distance=2.02 Simple disulfide: pdb=" SG CYS C 224 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 258 " - pdb=" SG CYS C 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 426 " - pdb=" SG CYS E 430 " distance=2.03 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 515 " - pdb=" SG CYS E 531 " distance=2.03 Simple disulfide: pdb=" SG CYS E 519 " - pdb=" SG CYS E 541 " distance=2.03 Simple disulfide: pdb=" SG CYS E 528 " - pdb=" SG CYS E 558 " distance=2.03 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 581 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 609 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 611 " - pdb=" SG CYS E 618 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 93 " distance=2.04 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 222 " distance=2.02 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 174 " distance=2.02 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 200 " distance=2.02 Simple disulfide: pdb=" SG CYS D 195 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 224 " - pdb=" SG CYS D 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 258 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 243 " distance=2.03 Simple disulfide: pdb=" SG CYS F 426 " - pdb=" SG CYS F 430 " distance=2.03 Simple disulfide: pdb=" SG CYS F 449 " - pdb=" SG CYS F 478 " distance=2.03 Simple disulfide: pdb=" SG CYS F 515 " - pdb=" SG CYS F 531 " distance=2.03 Simple disulfide: pdb=" SG CYS F 519 " - pdb=" SG CYS F 541 " distance=2.03 Simple disulfide: pdb=" SG CYS F 528 " - pdb=" SG CYS F 558 " distance=2.03 Simple disulfide: pdb=" SG CYS F 565 " - pdb=" SG CYS F 581 " distance=2.03 Simple disulfide: pdb=" SG CYS F 570 " - pdb=" SG CYS F 585 " distance=2.03 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS F 620 " distance=2.03 Simple disulfide: pdb=" SG CYS F 611 " - pdb=" SG CYS F 618 " distance=2.03 Simple disulfide: pdb=" SG CYS U 103 " - pdb=" SG CYS U 165 " distance=2.03 Simple disulfide: pdb=" SG CYS U 130 " - pdb=" SG CYS U 194 " distance=2.03 Simple disulfide: pdb=" SG CYS U 134 " - pdb=" SG CYS U 196 " distance=2.03 Simple disulfide: pdb=" SG CYS U 164 " - pdb=" SG CYS V 164 " distance=2.10 Simple disulfide: pdb=" SG CYS V 103 " - pdb=" SG CYS V 165 " distance=2.03 Simple disulfide: pdb=" SG CYS V 130 " - pdb=" SG CYS V 194 " distance=2.03 Simple disulfide: pdb=" SG CYS V 134 " - pdb=" SG CYS V 196 " distance=2.03 Simple disulfide: pdb=" SG CYS W 40 " - pdb=" SG CYS W 93 " distance=2.04 Simple disulfide: pdb=" SG CYS W 95 " - pdb=" SG CYS W 105 " distance=2.03 Simple disulfide: pdb=" SG CYS W 161 " - pdb=" SG CYS W 222 " distance=2.02 Simple disulfide: pdb=" SG CYS W 168 " - pdb=" SG CYS W 174 " distance=2.02 Simple disulfide: pdb=" SG CYS W 185 " - pdb=" SG CYS W 200 " distance=2.02 Simple disulfide: pdb=" SG CYS W 195 " - pdb=" SG CYS W 241 " distance=2.02 Simple disulfide: pdb=" SG CYS W 224 " - pdb=" SG CYS W 229 " distance=2.03 Simple disulfide: pdb=" SG CYS W 251 " - pdb=" SG CYS W 323 " distance=2.03 Simple disulfide: pdb=" SG CYS W 258 " - pdb=" SG CYS W 264 " distance=2.03 Simple disulfide: pdb=" SG CYS W 275 " - pdb=" SG CYS W 293 " distance=2.03 Simple disulfide: pdb=" SG CYS W 285 " - pdb=" SG CYS W 347 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 137 " - pdb=" SG CYS Y 142 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 157 " - pdb=" SG CYS Y 197 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 166 " - pdb=" SG CYS Y 243 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 426 " - pdb=" SG CYS Y 430 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 449 " - pdb=" SG CYS Y 478 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 515 " - pdb=" SG CYS Y 531 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 519 " - pdb=" SG CYS Y 541 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 528 " - pdb=" SG CYS Y 558 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 565 " - pdb=" SG CYS Y 581 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 570 " - pdb=" SG CYS Y 585 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 609 " - pdb=" SG CYS Y 620 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 611 " - pdb=" SG CYS Y 618 " distance=2.03 Simple disulfide: pdb=" SG CYS X 40 " - pdb=" SG CYS X 93 " distance=2.04 Simple disulfide: pdb=" SG CYS X 95 " - pdb=" SG CYS X 105 " distance=2.03 Simple disulfide: pdb=" SG CYS X 161 " - pdb=" SG CYS X 222 " distance=2.02 Simple disulfide: pdb=" SG CYS X 168 " - pdb=" SG CYS X 174 " distance=2.02 Simple disulfide: pdb=" SG CYS X 185 " - pdb=" SG CYS X 200 " distance=2.02 Simple disulfide: pdb=" SG CYS X 195 " - pdb=" SG CYS X 241 " distance=2.02 Simple disulfide: pdb=" SG CYS X 224 " - pdb=" SG CYS X 229 " distance=2.03 Simple disulfide: pdb=" SG CYS X 251 " - pdb=" SG CYS X 323 " distance=2.03 Simple disulfide: pdb=" SG CYS X 258 " - pdb=" SG CYS X 264 " distance=2.03 Simple disulfide: pdb=" SG CYS X 275 " - pdb=" SG CYS X 293 " distance=2.03 Simple disulfide: pdb=" SG CYS X 285 " - pdb=" SG CYS X 347 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 137 " - pdb=" SG CYS Z 142 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 157 " - pdb=" SG CYS Z 197 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 166 " - pdb=" SG CYS Z 243 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 426 " - pdb=" SG CYS Z 430 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 449 " - pdb=" SG CYS Z 478 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 515 " - pdb=" SG CYS Z 531 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 519 " - pdb=" SG CYS Z 541 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 528 " - pdb=" SG CYS Z 558 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 565 " - pdb=" SG CYS Z 581 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 570 " - pdb=" SG CYS Z 585 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 609 " - pdb=" SG CYS Z 620 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 611 " - pdb=" SG CYS Z 618 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E2005 " - " ASN E 377 " " NAG E2006 " - " ASN E 394 " " NAG E2007 " - " ASN E 468 " " NAG E2008 " - " ASN E 367 " " NAG E2009 " - " ASN E 336 " " NAG E2010 " - " ASN E 361 " " NAG F2005 " - " ASN F 377 " " NAG F2006 " - " ASN F 394 " " NAG F2007 " - " ASN F 468 " " NAG F2008 " - " ASN F 367 " " NAG F2009 " - " ASN F 336 " " NAG F2010 " - " ASN F 361 " " NAG Y2005 " - " ASN Y 377 " " NAG Y2006 " - " ASN Y 394 " " NAG Y2007 " - " ASN Y 468 " " NAG Y2008 " - " ASN Y 367 " " NAG Y2009 " - " ASN Y 336 " " NAG Y2010 " - " ASN Y 361 " " NAG Z2005 " - " ASN Z 377 " " NAG Z2006 " - " ASN Z 394 " " NAG Z2007 " - " ASN Z 468 " " NAG Z2008 " - " ASN Z 367 " " NAG Z2009 " - " ASN Z 336 " " NAG Z2010 " - " ASN Z 361 " Time building additional restraints: 11.40 Conformation dependent library (CDL) restraints added in 4.5 seconds 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7200 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 72 sheets defined 28.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.852A pdb=" N GLY A 116 " --> pdb=" O SER A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'B' and resid 113 through 116 Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 76 through 86 removed outlier: 3.598A pdb=" N ALA C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.601A pdb=" N ILE C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.678A pdb=" N LYS C 175 " --> pdb=" O ASN C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 208 removed outlier: 3.556A pdb=" N CYS C 200 " --> pdb=" O ASN C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.709A pdb=" N THR C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.686A pdb=" N ALA C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.602A pdb=" N ASP C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 275 removed outlier: 3.565A pdb=" N ASN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 288 Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.958A pdb=" N CYS C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 344 removed outlier: 3.725A pdb=" N ASP C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 Processing helix chain 'E' and resid 102 through 110 removed outlier: 4.132A pdb=" N TRP E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 114 removed outlier: 3.520A pdb=" N HIS E 114 " --> pdb=" O VAL E 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 114' Processing helix chain 'E' and resid 162 through 167 removed outlier: 3.800A pdb=" N PHE E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'E' and resid 322 through 328 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.879A pdb=" N ALA E 432 " --> pdb=" O ASN E 429 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE E 433 " --> pdb=" O CYS E 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 433' Processing helix chain 'E' and resid 470 through 475 Processing helix chain 'E' and resid 518 through 522 removed outlier: 3.788A pdb=" N VAL E 521 " --> pdb=" O SER E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 530 Processing helix chain 'E' and resid 564 through 568 removed outlier: 3.752A pdb=" N ASP E 567 " --> pdb=" O THR E 564 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY E 568 " --> pdb=" O CYS E 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 564 through 568' Processing helix chain 'E' and resid 581 through 586 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 76 through 86 removed outlier: 3.598A pdb=" N ALA D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.601A pdb=" N ILE D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 171 through 186 removed outlier: 3.677A pdb=" N LYS D 175 " --> pdb=" O ASN D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 removed outlier: 3.556A pdb=" N CYS D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.709A pdb=" N THR D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.686A pdb=" N ALA D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.602A pdb=" N ASP D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 275 removed outlier: 3.565A pdb=" N ASN D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 288 Processing helix chain 'D' and resid 289 through 299 removed outlier: 3.957A pdb=" N CYS D 293 " --> pdb=" O ASN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 removed outlier: 3.725A pdb=" N ASP D 341 " --> pdb=" O LYS D 337 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 Processing helix chain 'F' and resid 102 through 110 removed outlier: 4.132A pdb=" N TRP F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 114 removed outlier: 3.520A pdb=" N HIS F 114 " --> pdb=" O VAL F 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 111 through 114' Processing helix chain 'F' and resid 162 through 167 removed outlier: 3.800A pdb=" N PHE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'F' and resid 322 through 328 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.879A pdb=" N ALA F 432 " --> pdb=" O ASN F 429 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE F 433 " --> pdb=" O CYS F 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 433' Processing helix chain 'F' and resid 470 through 475 Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.788A pdb=" N VAL F 521 " --> pdb=" O SER F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 530 Processing helix chain 'F' and resid 564 through 568 removed outlier: 3.752A pdb=" N ASP F 567 " --> pdb=" O THR F 564 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY F 568 " --> pdb=" O CYS F 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 564 through 568' Processing helix chain 'F' and resid 581 through 586 Processing helix chain 'U' and resid 113 through 116 removed outlier: 3.852A pdb=" N GLY U 116 " --> pdb=" O SER U 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 113 through 116' Processing helix chain 'U' and resid 139 through 152 Processing helix chain 'V' and resid 113 through 116 Processing helix chain 'V' and resid 139 through 151 Processing helix chain 'W' and resid 39 through 49 Processing helix chain 'W' and resid 51 through 65 Processing helix chain 'W' and resid 76 through 86 removed outlier: 3.598A pdb=" N ALA W 81 " --> pdb=" O GLU W 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 112 removed outlier: 3.601A pdb=" N ILE W 112 " --> pdb=" O ILE W 108 " (cutoff:3.500A) Processing helix chain 'W' and resid 160 through 170 Processing helix chain 'W' and resid 171 through 186 removed outlier: 3.677A pdb=" N LYS W 175 " --> pdb=" O ASN W 171 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 208 removed outlier: 3.556A pdb=" N CYS W 200 " --> pdb=" O ASN W 196 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 221 removed outlier: 3.709A pdb=" N THR W 216 " --> pdb=" O PRO W 212 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG W 218 " --> pdb=" O GLU W 214 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 235 removed outlier: 3.686A pdb=" N ALA W 230 " --> pdb=" O ASP W 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 236 through 238 No H-bonds generated for 'chain 'W' and resid 236 through 238' Processing helix chain 'W' and resid 250 through 261 removed outlier: 3.602A pdb=" N ASP W 261 " --> pdb=" O VAL W 257 " (cutoff:3.500A) Processing helix chain 'W' and resid 261 through 275 removed outlier: 3.566A pdb=" N ASN W 274 " --> pdb=" O ASP W 270 " (cutoff:3.500A) Processing helix chain 'W' and resid 285 through 288 Processing helix chain 'W' and resid 289 through 299 removed outlier: 3.958A pdb=" N CYS W 293 " --> pdb=" O ASN W 289 " (cutoff:3.500A) Processing helix chain 'W' and resid 331 through 344 removed outlier: 3.725A pdb=" N ASP W 341 " --> pdb=" O LYS W 337 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE W 342 " --> pdb=" O PHE W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 345 through 357 Processing helix chain 'Y' and resid 102 through 110 removed outlier: 4.132A pdb=" N TRP Y 106 " --> pdb=" O ASP Y 102 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 114 removed outlier: 3.521A pdb=" N HIS Y 114 " --> pdb=" O VAL Y 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 111 through 114' Processing helix chain 'Y' and resid 162 through 167 removed outlier: 3.799A pdb=" N PHE Y 167 " --> pdb=" O ARG Y 163 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 197 Processing helix chain 'Y' and resid 309 through 313 Processing helix chain 'Y' and resid 322 through 328 Processing helix chain 'Y' and resid 429 through 433 removed outlier: 3.879A pdb=" N ALA Y 432 " --> pdb=" O ASN Y 429 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE Y 433 " --> pdb=" O CYS Y 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 429 through 433' Processing helix chain 'Y' and resid 470 through 475 Processing helix chain 'Y' and resid 518 through 522 removed outlier: 3.789A pdb=" N VAL Y 521 " --> pdb=" O SER Y 518 " (cutoff:3.500A) Processing helix chain 'Y' and resid 525 through 530 Processing helix chain 'Y' and resid 564 through 568 removed outlier: 3.752A pdb=" N ASP Y 567 " --> pdb=" O THR Y 564 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY Y 568 " --> pdb=" O CYS Y 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 564 through 568' Processing helix chain 'Y' and resid 581 through 586 Processing helix chain 'X' and resid 39 through 49 Processing helix chain 'X' and resid 51 through 65 Processing helix chain 'X' and resid 76 through 86 removed outlier: 3.598A pdb=" N ALA X 81 " --> pdb=" O GLU X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 112 removed outlier: 3.601A pdb=" N ILE X 112 " --> pdb=" O ILE X 108 " (cutoff:3.500A) Processing helix chain 'X' and resid 160 through 170 Processing helix chain 'X' and resid 171 through 186 removed outlier: 3.677A pdb=" N LYS X 175 " --> pdb=" O ASN X 171 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 208 removed outlier: 3.556A pdb=" N CYS X 200 " --> pdb=" O ASN X 196 " (cutoff:3.500A) Processing helix chain 'X' and resid 212 through 221 removed outlier: 3.709A pdb=" N THR X 216 " --> pdb=" O PRO X 212 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG X 218 " --> pdb=" O GLU X 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 235 removed outlier: 3.686A pdb=" N ALA X 230 " --> pdb=" O ASP X 226 " (cutoff:3.500A) Processing helix chain 'X' and resid 236 through 238 No H-bonds generated for 'chain 'X' and resid 236 through 238' Processing helix chain 'X' and resid 250 through 261 removed outlier: 3.602A pdb=" N ASP X 261 " --> pdb=" O VAL X 257 " (cutoff:3.500A) Processing helix chain 'X' and resid 261 through 275 removed outlier: 3.565A pdb=" N ASN X 274 " --> pdb=" O ASP X 270 " (cutoff:3.500A) Processing helix chain 'X' and resid 285 through 288 Processing helix chain 'X' and resid 289 through 299 removed outlier: 3.959A pdb=" N CYS X 293 " --> pdb=" O ASN X 289 " (cutoff:3.500A) Processing helix chain 'X' and resid 331 through 344 removed outlier: 3.724A pdb=" N ASP X 341 " --> pdb=" O LYS X 337 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE X 342 " --> pdb=" O PHE X 338 " (cutoff:3.500A) Processing helix chain 'X' and resid 345 through 357 Processing helix chain 'Z' and resid 102 through 110 removed outlier: 4.133A pdb=" N TRP Z 106 " --> pdb=" O ASP Z 102 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 114 removed outlier: 3.521A pdb=" N HIS Z 114 " --> pdb=" O VAL Z 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 111 through 114' Processing helix chain 'Z' and resid 162 through 167 removed outlier: 3.799A pdb=" N PHE Z 167 " --> pdb=" O ARG Z 163 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 197 Processing helix chain 'Z' and resid 309 through 313 Processing helix chain 'Z' and resid 322 through 328 Processing helix chain 'Z' and resid 429 through 433 removed outlier: 3.878A pdb=" N ALA Z 432 " --> pdb=" O ASN Z 429 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE Z 433 " --> pdb=" O CYS Z 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 429 through 433' Processing helix chain 'Z' and resid 470 through 475 Processing helix chain 'Z' and resid 518 through 522 removed outlier: 3.789A pdb=" N VAL Z 521 " --> pdb=" O SER Z 518 " (cutoff:3.500A) Processing helix chain 'Z' and resid 525 through 530 Processing helix chain 'Z' and resid 564 through 568 removed outlier: 3.752A pdb=" N ASP Z 567 " --> pdb=" O THR Z 564 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY Z 568 " --> pdb=" O CYS Z 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 564 through 568' Processing helix chain 'Z' and resid 581 through 586 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 111 Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 167 Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 111 Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 177 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AA9, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.694A pdb=" N LEU E 95 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 72 through 73 removed outlier: 3.824A pdb=" N HIS E 81 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 174 through 176 removed outlier: 3.876A pdb=" N PHE E 174 " --> pdb=" O PRO E 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR E 261 " --> pdb=" O PHE E 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.670A pdb=" N THR E 184 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR E 225 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS E 186 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 280 through 283 Processing sheet with id=AB7, first strand: chain 'E' and resid 292 through 300 removed outlier: 6.349A pdb=" N LEU E 356 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR E 295 " --> pdb=" O TYR E 354 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR E 354 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG E 297 " --> pdb=" O HIS E 352 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS E 352 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE E 299 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR E 350 " --> pdb=" O PHE E 299 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 410 through 413 removed outlier: 7.547A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLU E 505 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 486 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 421 through 425 removed outlier: 7.201A pdb=" N GLN E 421 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL E 467 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY E 423 " --> pdb=" O LEU E 465 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AC2, first strand: chain 'E' and resid 589 through 591 Processing sheet with id=AC3, first strand: chain 'E' and resid 595 through 596 Processing sheet with id=AC4, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.695A pdb=" N LEU F 95 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 72 through 73 removed outlier: 3.824A pdb=" N HIS F 81 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 174 through 176 removed outlier: 3.876A pdb=" N PHE F 174 " --> pdb=" O PRO F 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR F 261 " --> pdb=" O PHE F 174 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.670A pdb=" N THR F 184 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR F 225 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS F 186 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 280 through 283 Processing sheet with id=AD4, first strand: chain 'F' and resid 292 through 300 removed outlier: 6.350A pdb=" N LEU F 356 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR F 295 " --> pdb=" O TYR F 354 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR F 354 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG F 297 " --> pdb=" O HIS F 352 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS F 352 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE F 299 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR F 350 " --> pdb=" O PHE F 299 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 410 through 413 removed outlier: 7.546A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLU F 505 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 486 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 425 removed outlier: 7.201A pdb=" N GLN F 421 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL F 467 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY F 423 " --> pdb=" O LEU F 465 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD8, first strand: chain 'F' and resid 589 through 591 Processing sheet with id=AD9, first strand: chain 'F' and resid 595 through 596 Processing sheet with id=AE1, first strand: chain 'U' and resid 104 through 111 Processing sheet with id=AE2, first strand: chain 'U' and resid 165 through 167 Processing sheet with id=AE3, first strand: chain 'U' and resid 173 through 177 Processing sheet with id=AE4, first strand: chain 'V' and resid 104 through 111 Processing sheet with id=AE5, first strand: chain 'V' and resid 165 through 167 Processing sheet with id=AE6, first strand: chain 'V' and resid 173 through 177 Processing sheet with id=AE7, first strand: chain 'W' and resid 308 through 309 Processing sheet with id=AE8, first strand: chain 'Y' and resid 30 through 31 Processing sheet with id=AE9, first strand: chain 'Y' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR Y 36 " --> pdb=" O TYR Y 146 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER Y 148 " --> pdb=" O TYR Y 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR Y 36 " --> pdb=" O TYR Y 146 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER Y 148 " --> pdb=" O TYR Y 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 49 through 52 removed outlier: 6.695A pdb=" N LEU Y 95 " --> pdb=" O LEU Y 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 72 through 73 removed outlier: 3.823A pdb=" N HIS Y 81 " --> pdb=" O LEU Y 72 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 174 through 176 removed outlier: 3.876A pdb=" N PHE Y 174 " --> pdb=" O PRO Y 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR Y 261 " --> pdb=" O PHE Y 174 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 184 through 187 removed outlier: 6.670A pdb=" N THR Y 184 " --> pdb=" O THR Y 225 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR Y 225 " --> pdb=" O THR Y 184 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS Y 186 " --> pdb=" O VAL Y 223 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 280 through 283 Processing sheet with id=AF7, first strand: chain 'Y' and resid 292 through 300 removed outlier: 6.350A pdb=" N LEU Y 356 " --> pdb=" O VAL Y 293 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR Y 295 " --> pdb=" O TYR Y 354 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR Y 354 " --> pdb=" O THR Y 295 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG Y 297 " --> pdb=" O HIS Y 352 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS Y 352 " --> pdb=" O ARG Y 297 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE Y 299 " --> pdb=" O THR Y 350 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR Y 350 " --> pdb=" O PHE Y 299 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 410 through 413 removed outlier: 7.548A pdb=" N LEU Y 410 " --> pdb=" O THR Y 503 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLU Y 505 " --> pdb=" O LEU Y 410 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL Y 412 " --> pdb=" O GLU Y 505 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL Y 486 " --> pdb=" O LYS Y 441 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 421 through 425 removed outlier: 7.201A pdb=" N GLN Y 421 " --> pdb=" O VAL Y 467 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL Y 467 " --> pdb=" O GLN Y 421 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY Y 423 " --> pdb=" O LEU Y 465 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 542 through 544 Processing sheet with id=AG2, first strand: chain 'Y' and resid 589 through 591 Processing sheet with id=AG3, first strand: chain 'Y' and resid 595 through 596 Processing sheet with id=AG4, first strand: chain 'X' and resid 308 through 309 Processing sheet with id=AG5, first strand: chain 'Z' and resid 30 through 31 Processing sheet with id=AG6, first strand: chain 'Z' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR Z 36 " --> pdb=" O TYR Z 146 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER Z 148 " --> pdb=" O TYR Z 36 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 35 through 36 removed outlier: 6.135A pdb=" N TYR Z 36 " --> pdb=" O TYR Z 146 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER Z 148 " --> pdb=" O TYR Z 36 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 49 through 52 removed outlier: 6.694A pdb=" N LEU Z 95 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 72 through 73 removed outlier: 3.823A pdb=" N HIS Z 81 " --> pdb=" O LEU Z 72 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 174 through 176 removed outlier: 3.877A pdb=" N PHE Z 174 " --> pdb=" O PRO Z 259 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR Z 261 " --> pdb=" O PHE Z 174 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 184 through 187 removed outlier: 6.669A pdb=" N THR Z 184 " --> pdb=" O THR Z 225 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR Z 225 " --> pdb=" O THR Z 184 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS Z 186 " --> pdb=" O VAL Z 223 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 280 through 283 Processing sheet with id=AH4, first strand: chain 'Z' and resid 292 through 300 removed outlier: 6.351A pdb=" N LEU Z 356 " --> pdb=" O VAL Z 293 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR Z 295 " --> pdb=" O TYR Z 354 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR Z 354 " --> pdb=" O THR Z 295 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG Z 297 " --> pdb=" O HIS Z 352 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS Z 352 " --> pdb=" O ARG Z 297 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE Z 299 " --> pdb=" O THR Z 350 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR Z 350 " --> pdb=" O PHE Z 299 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 410 through 413 removed outlier: 7.548A pdb=" N LEU Z 410 " --> pdb=" O THR Z 503 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLU Z 505 " --> pdb=" O LEU Z 410 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL Z 412 " --> pdb=" O GLU Z 505 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Z 486 " --> pdb=" O LYS Z 441 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 421 through 425 removed outlier: 7.201A pdb=" N GLN Z 421 " --> pdb=" O VAL Z 467 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL Z 467 " --> pdb=" O GLN Z 421 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY Z 423 " --> pdb=" O LEU Z 465 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Z' and resid 542 through 544 Processing sheet with id=AH8, first strand: chain 'Z' and resid 589 through 591 Processing sheet with id=AH9, first strand: chain 'Z' and resid 595 through 596 1004 hydrogen bonds defined for protein. 2778 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: 11.72 Time building geometry restraints manager: 12.33 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: 10281 1.34 - 1.46: 7183 1.46 - 1.59: 13236 1.59 - 1.71: 0 1.71 - 1.83: 308 Bond restraints: 31008 Sorted by residual: bond pdb=" C CYS Z 565 " pdb=" N PRO Z 566 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.75e+00 bond pdb=" C CYS Y 565 " pdb=" N PRO Y 566 " ideal model delta sigma weight residual 1.334 1.389 -0.056 2.34e-02 1.83e+03 5.64e+00 bond pdb=" C CYS F 565 " pdb=" N PRO F 566 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.62e+00 bond pdb=" C CYS E 565 " pdb=" N PRO E 566 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.60e+00 bond pdb=" C1 NAG F2005 " pdb=" O5 NAG F2005 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 ... (remaining 31003 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.04: 760 106.04 - 113.03: 16476 113.03 - 120.01: 10615 120.01 - 127.00: 13786 127.00 - 133.98: 355 Bond angle restraints: 41992 Sorted by residual: angle pdb=" N VAL Z 303 " pdb=" CA VAL Z 303 " pdb=" C VAL Z 303 " ideal model delta sigma weight residual 113.53 107.00 6.53 9.80e-01 1.04e+00 4.44e+01 angle pdb=" N VAL Y 303 " pdb=" CA VAL Y 303 " pdb=" C VAL Y 303 " ideal model delta sigma weight residual 113.53 107.02 6.51 9.80e-01 1.04e+00 4.41e+01 angle pdb=" N VAL F 303 " pdb=" CA VAL F 303 " pdb=" C VAL F 303 " ideal model delta sigma weight residual 113.53 107.03 6.50 9.80e-01 1.04e+00 4.40e+01 angle pdb=" N VAL E 303 " pdb=" CA VAL E 303 " pdb=" C VAL E 303 " ideal model delta sigma weight residual 113.53 107.05 6.48 9.80e-01 1.04e+00 4.38e+01 angle pdb=" N ASN Y 448 " pdb=" CA ASN Y 448 " pdb=" C ASN Y 448 " ideal model delta sigma weight residual 114.75 109.97 4.78 1.26e+00 6.30e-01 1.44e+01 ... (remaining 41987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 18253 16.02 - 32.05: 531 32.05 - 48.07: 134 48.07 - 64.10: 10 64.10 - 80.12: 22 Dihedral angle restraints: 18950 sinusoidal: 7842 harmonic: 11108 Sorted by residual: dihedral pdb=" CB CYS Z 426 " pdb=" SG CYS Z 426 " pdb=" SG CYS Z 430 " pdb=" CB CYS Z 430 " ideal model delta sinusoidal sigma weight residual -86.00 -166.12 80.12 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS Y 426 " pdb=" SG CYS Y 426 " pdb=" SG CYS Y 430 " pdb=" CB CYS Y 430 " ideal model delta sinusoidal sigma weight residual -86.00 -166.11 80.11 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS F 426 " pdb=" SG CYS F 426 " pdb=" SG CYS F 430 " pdb=" CB CYS F 430 " ideal model delta sinusoidal sigma weight residual -86.00 -166.10 80.10 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 18947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2647 0.034 - 0.069: 1329 0.069 - 0.103: 455 0.103 - 0.137: 185 0.137 - 0.172: 32 Chirality restraints: 4648 Sorted by residual: chirality pdb=" CB VAL Z 340 " pdb=" CA VAL Z 340 " pdb=" CG1 VAL Z 340 " pdb=" CG2 VAL Z 340 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CB VAL Y 340 " pdb=" CA VAL Y 340 " pdb=" CG1 VAL Y 340 " pdb=" CG2 VAL Y 340 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CB VAL E 340 " pdb=" CA VAL E 340 " pdb=" CG1 VAL E 340 " pdb=" CG2 VAL E 340 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 4645 not shown) Planarity restraints: 5524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 320 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO D 321 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 320 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO W 321 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO W 321 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO W 321 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 320 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO C 321 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " 0.028 5.00e-02 4.00e+02 ... (remaining 5521 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 28 2.09 - 2.79: 7103 2.79 - 3.49: 37315 3.49 - 4.20: 68052 4.20 - 4.90: 114948 Nonbonded interactions: 227446 Sorted by model distance: nonbonded pdb=" OD2 ASP F 300 " pdb=" OH TYR F 314 " model vdw 1.384 2.440 nonbonded pdb=" OD2 ASP Y 300 " pdb=" OH TYR Y 314 " model vdw 1.384 2.440 nonbonded pdb=" OD2 ASP Z 300 " pdb=" OH TYR Z 314 " model vdw 1.384 2.440 nonbonded pdb=" OD2 ASP E 300 " pdb=" OH TYR E 314 " model vdw 1.384 2.440 nonbonded pdb=" OD1 ASP Y 230 " pdb=" OE1 GLU Y 232 " model vdw 1.698 3.040 ... (remaining 227441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.870 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 76.270 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5354 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 : 0.004 0.056 31008 Z= 0.293 Angle : 0.823 7.209 41992 Z= 0.479 Chirality : 0.048 0.172 4648 Planarity : 0.006 0.052 5500 Dihedral : 8.430 76.248 11432 Min Nonbonded Distance : 1.384 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.11), residues: 3720 helix: -2.84 (0.11), residues: 888 sheet: -1.79 (0.16), residues: 944 loop : -2.82 (0.12), residues: 1888 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 576 time to evaluate : 3.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.5634 time to fit residues: 472.4548 Evaluate side-chains 200 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.715 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.8980 chunk 284 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 294 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 341 optimal weight: 30.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN E 246 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN F 443 HIS F 482 HIS F 554 ASN W 274 ASN W 330 ASN Y 246 HIS ** Y 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 443 HIS Z 103 HIS Z 333 HIS Z 443 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 31008 Z= 0.213 Angle : 0.599 12.060 41992 Z= 0.308 Chirality : 0.041 0.252 4648 Planarity : 0.005 0.054 5500 Dihedral : 4.823 22.085 4252 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.57 (0.12), residues: 3720 helix: -0.94 (0.15), residues: 904 sheet: -1.34 (0.16), residues: 976 loop : -2.30 (0.13), residues: 1840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.4979 time to fit residues: 199.9200 Evaluate side-chains 127 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 3.782 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 0.9980 chunk 105 optimal weight: 40.0000 chunk 284 optimal weight: 0.9990 chunk 232 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 342 optimal weight: 0.6980 chunk 369 optimal weight: 0.4980 chunk 304 optimal weight: 1.9990 chunk 339 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 272 HIS W 330 ASN ** Y 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 341 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 31008 Z= 0.120 Angle : 0.519 11.345 41992 Z= 0.260 Chirality : 0.040 0.234 4648 Planarity : 0.004 0.039 5500 Dihedral : 4.317 26.821 4252 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.86 (0.13), residues: 3720 helix: -0.05 (0.17), residues: 936 sheet: -0.90 (0.17), residues: 928 loop : -2.05 (0.13), residues: 1856 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 4.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 235 average time/residue: 0.4754 time to fit residues: 174.1578 Evaluate side-chains 129 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 3.790 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 343 optimal weight: 0.0170 chunk 363 optimal weight: 40.0000 chunk 179 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN C 272 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 ASN E 403 HIS D 62 GLN D 201 HIS D 350 ASN ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 GLN ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN Y 326 GLN ** Y 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 343 ASN Y 437 ASN ** Y 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 ASN X 201 HIS ** X 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 330 ASN X 350 ASN Z 54 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 31008 Z= 0.243 Angle : 0.647 13.254 41992 Z= 0.332 Chirality : 0.042 0.193 4648 Planarity : 0.005 0.050 5500 Dihedral : 4.776 22.791 4252 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.84 (0.13), residues: 3720 helix: -0.06 (0.17), residues: 940 sheet: -0.93 (0.16), residues: 976 loop : -2.03 (0.13), residues: 1804 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 4.843 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: 3 outliers final: 0 residues processed: 198 average time/residue: 0.4827 time to fit residues: 152.7023 Evaluate side-chains 99 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 3.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 5.9990 chunk 206 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 270 optimal weight: 20.0000 chunk 149 optimal weight: 50.0000 chunk 310 optimal weight: 8.9990 chunk 251 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 185 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 272 HIS E 84 ASN E 138 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 HIS D 62 GLN D 169 ASN D 227 GLN D 272 HIS D 330 ASN ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN F 437 ASN W 86 GLN W 201 HIS W 262 HIS W 330 ASN Y 84 ASN Y 138 GLN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 443 HIS ** Y 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 272 HIS ** X 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.8872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 31008 Z= 0.388 Angle : 0.873 11.797 41992 Z= 0.452 Chirality : 0.049 0.252 4648 Planarity : 0.008 0.129 5500 Dihedral : 6.263 33.981 4252 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 27.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.52 (0.13), residues: 3720 helix: -0.96 (0.16), residues: 920 sheet: -1.33 (0.16), residues: 964 loop : -2.23 (0.13), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 163 average time/residue: 0.4589 time to fit residues: 120.6220 Evaluate side-chains 101 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 3.869 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2855 time to fit residues: 6.0754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 6.9990 chunk 327 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 363 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 482 HIS D 62 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 186 HIS F 326 GLN F 333 HIS W 113 HIS ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 482 HIS X 308 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.9114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 31008 Z= 0.206 Angle : 0.610 12.027 41992 Z= 0.312 Chirality : 0.042 0.188 4648 Planarity : 0.005 0.051 5500 Dihedral : 5.254 36.951 4252 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.98 (0.13), residues: 3720 helix: -0.22 (0.17), residues: 908 sheet: -1.10 (0.16), residues: 964 loop : -2.00 (0.14), residues: 1848 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 150 average time/residue: 0.4702 time to fit residues: 113.6323 Evaluate side-chains 96 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 3.815 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 362 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 437 ASN Z 594 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 1.0011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 31008 Z= 0.254 Angle : 0.669 12.896 41992 Z= 0.344 Chirality : 0.043 0.193 4648 Planarity : 0.006 0.088 5500 Dihedral : 5.427 32.450 4252 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.02 (0.13), residues: 3720 helix: -0.27 (0.17), residues: 900 sheet: -1.25 (0.16), residues: 1004 loop : -1.93 (0.14), residues: 1816 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 4.153 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: 1 outliers final: 0 residues processed: 136 average time/residue: 0.4572 time to fit residues: 102.7702 Evaluate side-chains 88 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 3.854 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 0.9980 chunk 144 optimal weight: 0.4980 chunk 216 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 179 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 284 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 HIS E 84 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN F 103 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 84 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.9933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 31008 Z= 0.139 Angle : 0.556 10.985 41992 Z= 0.280 Chirality : 0.041 0.195 4648 Planarity : 0.004 0.050 5500 Dihedral : 4.736 36.287 4252 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.51 (0.14), residues: 3720 helix: 0.29 (0.17), residues: 904 sheet: -0.89 (0.17), residues: 972 loop : -1.73 (0.14), residues: 1844 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.4466 time to fit residues: 110.0291 Evaluate side-chains 95 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 4.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 40.0000 chunk 347 optimal weight: 40.0000 chunk 316 optimal weight: 30.0000 chunk 337 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 319 optimal weight: 9.9990 chunk 336 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 HIS E 84 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 HIS ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN D 62 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 HIS Y 84 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 272 HIS ** X 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 1.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 31008 Z= 0.295 Angle : 0.724 13.590 41992 Z= 0.369 Chirality : 0.045 0.200 4648 Planarity : 0.006 0.084 5500 Dihedral : 5.576 29.471 4252 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 24.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.93 (0.13), residues: 3720 helix: -0.24 (0.17), residues: 900 sheet: -1.10 (0.17), residues: 944 loop : -1.89 (0.14), residues: 1876 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 3.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.4441 time to fit residues: 85.1482 Evaluate side-chains 86 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 3.962 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 5.9990 chunk 357 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 374 optimal weight: 20.0000 chunk 344 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 159 ASN D 272 HIS D 330 ASN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 341 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 1.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 31008 Z= 0.217 Angle : 0.633 12.712 41992 Z= 0.322 Chirality : 0.043 0.195 4648 Planarity : 0.005 0.056 5500 Dihedral : 5.268 34.062 4252 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.89 (0.13), residues: 3720 helix: -0.24 (0.17), residues: 932 sheet: -1.08 (0.17), residues: 956 loop : -1.87 (0.14), residues: 1832 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.4246 time to fit residues: 85.5289 Evaluate side-chains 88 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 3.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 30.0000 chunk 317 optimal weight: 5.9990 chunk 91 optimal weight: 0.1980 chunk 275 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 306 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 HIS ** X 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 330 ASN ** 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 = 0.3917 r_free = 0.3917 target = 0.061784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.050701 restraints weight = 315176.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.051844 restraints weight = 188984.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.052625 restraints weight = 129050.438| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 1.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 31008 Z= 0.213 Angle : 0.626 13.363 41992 Z= 0.318 Chirality : 0.043 0.212 4648 Planarity : 0.005 0.109 5500 Dihedral : 5.147 31.809 4252 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.75 (0.14), residues: 3720 helix: 0.00 (0.17), residues: 908 sheet: -1.08 (0.17), residues: 960 loop : -1.79 (0.14), residues: 1852 =============================================================================== Job complete usr+sys time: 4592.60 seconds wall clock time: 85 minutes 47.11 seconds (5147.11 seconds total)