Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:30:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/12_2022/6q2r_20578_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/12_2022/6q2r_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_20578/12_2022/6q2r_20578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/12_2022/6q2r_20578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/12_2022/6q2r_20578_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2r_20578/12_2022/6q2r_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 Convert atoms to be neutral 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-dev-4807/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: 16.59, per 1000 atoms: 0.55 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: 11.96 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: 1.96 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: 10.57 Time building geometry restraints manager: 13.03 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=" C CYS B 134 " pdb=" N GLU B 135 " ideal model delta sigma weight residual 1.333 1.306 0.026 1.52e-02 4.33e+03 3.00e+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: 18397 16.02 - 32.05: 531 32.05 - 48.07: 134 48.07 - 64.10: 10 64.10 - 80.12: 22 Dihedral angle restraints: 19094 sinusoidal: 7986 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 19091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2695 0.034 - 0.069: 1305 0.069 - 0.103: 442 0.103 - 0.137: 174 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 7.780 Check model and map are aligned: 0.510 Convert atoms to be neutral: 0.280 Process input model: 75.270 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5311 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= 0.277 Angle : 0.810 7.209 41992 Z= 0.477 Chirality : 0.047 0.172 4648 Planarity : 0.006 0.052 5500 Dihedral : 8.413 76.248 11576 Min Nonbonded Distance : 1.384 Molprobity Statistics. All-atom Clashscore : 4.93 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 : 3.918 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: 0.5251 time to fit residues: 444.1732 Evaluate side-chains 200 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.634 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9040 ------------------------------------------------------------------------------- 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: 7.9990 chunk 219 optimal weight: 4.9990 chunk 341 optimal weight: 30.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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** D 107 GLN D 350 ASN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** X 350 ASN Z 103 HIS Z 333 HIS Z 443 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 31008 Z= 0.244 Angle : 0.656 12.026 41992 Z= 0.343 Chirality : 0.042 0.254 4648 Planarity : 0.006 0.066 5500 Dihedral : 5.113 21.698 4396 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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: -0.92 (0.15), residues: 900 sheet: -1.43 (0.16), residues: 964 loop : -2.25 (0.13), residues: 1856 *********************** 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 255 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 3.822 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: 255 average time/residue: 0.4668 time to fit residues: 183.4700 Evaluate side-chains 124 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 3.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0832 ------------------------------------------------------------------------------- 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: 0.0470 chunk 105 optimal weight: 8.9990 chunk 284 optimal weight: 8.9990 chunk 232 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 342 optimal weight: 8.9990 chunk 369 optimal weight: 20.0000 chunk 304 optimal weight: 0.6980 chunk 339 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 274 optimal weight: 30.0000 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 482 HIS D 62 GLN F 327 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 31008 Z= 0.128 Angle : 0.515 11.132 41992 Z= 0.261 Chirality : 0.040 0.232 4648 Planarity : 0.004 0.042 5500 Dihedral : 4.498 29.350 4396 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % 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: -1.85 (0.13), residues: 3720 helix: 0.10 (0.17), residues: 908 sheet: -1.02 (0.16), residues: 972 loop : -2.04 (0.13), residues: 1840 *********************** 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 211 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 3.782 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 outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.4230 time to fit residues: 144.3179 Evaluate side-chains 115 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.685 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0593 ------------------------------------------------------------------------------- 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: 50.0000 chunk 257 optimal weight: 30.0000 chunk 177 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 229 optimal weight: 30.0000 chunk 343 optimal weight: 20.0000 chunk 363 optimal weight: 30.0000 chunk 179 optimal weight: 30.0000 chunk 325 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS E 84 ASN E 103 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 429 ASN F 437 ASN W 201 HIS W 262 HIS ** W 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 103 HIS ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 326 GLN ** Y 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 308 ASN ** X 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 54 HIS ** Z 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.138 31008 Z= 0.412 Angle : 0.895 14.070 41992 Z= 0.468 Chirality : 0.050 0.307 4648 Planarity : 0.008 0.103 5500 Dihedral : 6.385 30.395 4396 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 29.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % 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: -2.51 (0.13), residues: 3720 helix: -0.94 (0.16), residues: 928 sheet: -1.20 (0.16), residues: 968 loop : -2.31 (0.13), residues: 1824 *********************** 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 173 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 3.746 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 outliers start: 5 outliers final: 1 residues processed: 172 average time/residue: 0.4519 time to fit residues: 124.0946 Evaluate side-chains 103 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 3.722 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2938 time to fit residues: 5.5771 ------------------------------------------------------------------------------- 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: 3.9990 chunk 206 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 270 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 chunk 310 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 326 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 HIS C 262 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN D 201 HIS F 333 HIS ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN Y 84 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 482 HIS X 272 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.8417 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= 0.222 Angle : 0.620 11.674 41992 Z= 0.322 Chirality : 0.043 0.268 4648 Planarity : 0.005 0.058 5500 Dihedral : 5.411 36.607 4396 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -2.07 (0.13), residues: 3720 helix: -0.33 (0.16), residues: 924 sheet: -1.08 (0.16), residues: 964 loop : -2.09 (0.13), residues: 1832 *********************** 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 152 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.4358 time to fit residues: 107.2552 Evaluate side-chains 98 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 3.714 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9560 ------------------------------------------------------------------------------- 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: 9.9990 chunk 71 optimal weight: 30.0000 chunk 213 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 363 optimal weight: 30.0000 chunk 301 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS W 330 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.9372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 31008 Z= 0.243 Angle : 0.645 13.651 41992 Z= 0.335 Chirality : 0.043 0.276 4648 Planarity : 0.005 0.066 5500 Dihedral : 5.431 32.525 4396 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % 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: -2.02 (0.13), residues: 3720 helix: -0.25 (0.17), residues: 924 sheet: -1.14 (0.16), residues: 996 loop : -2.02 (0.14), residues: 1800 *********************** 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 144 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.4341 time to fit residues: 102.6844 Evaluate side-chains 96 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 3.931 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0693 ------------------------------------------------------------------------------- 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: 40.0000 chunk 41 optimal weight: 6.9990 chunk 207 optimal weight: 0.2980 chunk 265 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 306 optimal weight: 20.0000 chunk 203 optimal weight: 4.9990 chunk 362 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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 330 ASN W 62 GLN W 330 ASN ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.9715 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= 0.193 Angle : 0.576 12.457 41992 Z= 0.298 Chirality : 0.042 0.238 4648 Planarity : 0.005 0.055 5500 Dihedral : 5.143 34.901 4396 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: -1.83 (0.13), residues: 3720 helix: -0.02 (0.17), residues: 928 sheet: -1.04 (0.16), residues: 1000 loop : -1.96 (0.14), residues: 1792 *********************** 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 137 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 3.736 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: 2 outliers final: 0 residues processed: 136 average time/residue: 0.4120 time to fit residues: 93.9044 Evaluate side-chains 92 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.602 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.1667 > 50: distance: 67 - 89: 15.998 distance: 85 - 89: 14.703 distance: 89 - 90: 11.302 distance: 90 - 91: 29.017 distance: 90 - 93: 17.977 distance: 91 - 92: 16.011 distance: 91 - 95: 32.729 distance: 93 - 94: 26.521 distance: 94 - 223: 5.602 distance: 95 - 96: 43.709 distance: 96 - 97: 19.649 distance: 96 - 99: 23.860 distance: 97 - 98: 17.710 distance: 97 - 106: 36.252 distance: 99 - 100: 17.609 distance: 100 - 101: 13.041 distance: 100 - 102: 7.304 distance: 101 - 103: 17.108 distance: 102 - 104: 16.457 distance: 103 - 105: 22.220 distance: 104 - 105: 26.245 distance: 106 - 107: 13.064 distance: 106 - 112: 9.892 distance: 107 - 108: 20.473 distance: 107 - 110: 14.651 distance: 108 - 109: 14.056 distance: 108 - 113: 27.515 distance: 110 - 111: 25.106 distance: 111 - 112: 20.070 distance: 113 - 114: 3.568 distance: 114 - 115: 4.487 distance: 114 - 117: 5.250 distance: 115 - 116: 7.140 distance: 115 - 122: 8.614 distance: 117 - 118: 5.733 distance: 118 - 119: 3.351 distance: 119 - 120: 7.017 distance: 119 - 121: 5.018 distance: 122 - 123: 3.199 distance: 123 - 124: 9.667 distance: 123 - 126: 4.862 distance: 124 - 125: 7.016 distance: 124 - 129: 10.508 distance: 126 - 127: 3.037 distance: 126 - 128: 13.410 distance: 129 - 130: 8.332 distance: 130 - 131: 18.263 distance: 130 - 133: 7.702 distance: 131 - 132: 19.183 distance: 131 - 140: 39.403 distance: 133 - 134: 19.896 distance: 134 - 135: 14.797 distance: 135 - 136: 12.155 distance: 136 - 137: 4.256 distance: 137 - 138: 5.370 distance: 140 - 141: 10.829 distance: 140 - 146: 13.972 distance: 141 - 142: 9.390 distance: 141 - 144: 7.932 distance: 142 - 147: 36.425 distance: 144 - 145: 9.364 distance: 145 - 146: 14.740 distance: 147 - 148: 26.366 distance: 148 - 149: 10.337 distance: 148 - 151: 10.736 distance: 149 - 150: 10.397 distance: 149 - 153: 21.763 distance: 151 - 152: 17.548 distance: 153 - 154: 5.373 distance: 154 - 155: 8.665 distance: 154 - 157: 3.732 distance: 155 - 156: 6.356 distance: 155 - 164: 6.462 distance: 157 - 158: 5.192 distance: 158 - 159: 3.012 distance: 158 - 160: 6.052 distance: 159 - 161: 3.386 distance: 160 - 162: 8.620 distance: 161 - 163: 7.160 distance: 162 - 163: 6.559 distance: 164 - 165: 6.859 distance: 165 - 166: 10.913 distance: 165 - 168: 9.716 distance: 166 - 167: 5.771 distance: 166 - 175: 20.270 distance: 168 - 169: 5.368 distance: 169 - 170: 6.425 distance: 171 - 172: 4.270 distance: 172 - 173: 3.371 distance: 172 - 174: 4.970