Starting phenix.real_space_refine on Tue Apr 9 16:01:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/04_2024/7qn6_14068_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/04_2024/7qn6_14068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/04_2024/7qn6_14068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/04_2024/7qn6_14068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/04_2024/7qn6_14068_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/04_2024/7qn6_14068_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 10941 2.51 5 N 2701 2.21 5 O 3087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16821 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2749 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2683 Chain: "B" Number of atoms: 2764 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2664 Chain: "C" Number of atoms: 2765 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2663 Chain: "D" Number of atoms: 2716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2721 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2592 Classifications: {'peptide': 324} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 310} Chain breaks: 1 Chain: "K" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N ALEU A 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 125 " occ=0.50 residue: pdb=" N ASER A 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 209 " occ=0.50 residue: pdb=" N ALEU A 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 214 " occ=0.50 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N ASER B 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 209 " occ=0.50 residue: pdb=" N ALEU B 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 214 " occ=0.50 residue: pdb=" N ASER B 229 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 229 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N ATYR C 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 66 " occ=0.50 residue: pdb=" N ALEU C 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 125 " occ=0.50 residue: pdb=" N ASER C 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 209 " occ=0.50 residue: pdb=" N ASER D 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 209 " occ=0.50 Time building chain proxies: 12.95, per 1000 atoms: 0.77 Number of scatterers: 16821 At special positions: 0 Unit cell: (118.272, 135.296, 124.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3087 8.00 N 2701 7.00 C 10941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 483 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG E 501 " - " ASN E 103 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 149 " " NAG H 1 " - " ASN C 149 " " NAG I 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 80 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 7.19 Conformation dependent library (CDL) restraints added in 4.8 seconds 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 28 sheets defined 31.5% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.501A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.571A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.679A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.733A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 306 Processing helix chain 'A' and resid 423 through 446 removed outlier: 3.525A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.500A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.572A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.678A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.732A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 306 Processing helix chain 'B' and resid 423 through 446 removed outlier: 3.525A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.501A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.572A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.678A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.733A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 306 Processing helix chain 'C' and resid 423 through 446 removed outlier: 3.524A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.500A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.570A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.678A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.732A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 306 Processing helix chain 'D' and resid 423 through 446 removed outlier: 3.524A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 118 removed outlier: 4.105A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 203 No H-bonds generated for 'chain 'E' and resid 200 through 203' Processing helix chain 'E' and resid 249 through 270 removed outlier: 3.734A pdb=" N SER E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) Proline residue: E 257 - end of helix removed outlier: 4.041A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 299 Processing helix chain 'E' and resid 309 through 335 Processing helix chain 'E' and resid 425 through 450 Proline residue: E 436 - end of helix Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'L' and resid 496 through 498 No H-bonds generated for 'chain 'L' and resid 496 through 498' Processing helix chain 'M' and resid 496 through 498 No H-bonds generated for 'chain 'M' and resid 496 through 498' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.270A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.029A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.681A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.271A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.028A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.682A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.271A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 49 through 51 removed outlier: 4.028A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.681A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.270A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.028A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.868A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.682A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 192 through 196 removed outlier: 6.181A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE E 144 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 124 through 126 removed outlier: 3.978A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 129 through 134 removed outlier: 6.769A pdb=" N THR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA E 132 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR E 159 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 2 through 7 Processing sheet with id= U, first strand: chain 'K' and resid 506 through 508 removed outlier: 3.860A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG K 425 " --> pdb=" O PHE K 434 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE K 434 " --> pdb=" O ARG K 425 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 484 through 486 removed outlier: 3.853A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 2 through 7 Processing sheet with id= X, first strand: chain 'L' and resid 506 through 508 removed outlier: 3.860A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 484 through 486 removed outlier: 3.852A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 2 through 7 Processing sheet with id= AA, first strand: chain 'M' and resid 506 through 508 removed outlier: 3.859A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 484 through 486 removed outlier: 3.852A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 7.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5100 1.34 - 1.46: 4382 1.46 - 1.58: 7662 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 17300 Sorted by residual: bond pdb=" C10 EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.804 1.766 0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C10 EPE D 501 " pdb=" S EPE D 501 " ideal model delta sigma weight residual 1.804 1.767 0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" O3S EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.477 1.441 0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" C10 EPE B 501 " pdb=" S EPE B 501 " ideal model delta sigma weight residual 1.804 1.768 0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" O2S EPE C 501 " pdb=" S EPE C 501 " ideal model delta sigma weight residual 1.477 1.442 0.035 2.00e-02 2.50e+03 3.05e+00 ... (remaining 17295 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 501 107.08 - 113.82: 9752 113.82 - 120.55: 6655 120.55 - 127.29: 6493 127.29 - 134.03: 194 Bond angle restraints: 23595 Sorted by residual: angle pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " pdb=" C5 BMA F 3 " ideal model delta sigma weight residual 118.82 113.42 5.40 3.00e+00 1.11e-01 3.25e+00 angle pdb=" C1 BMA G 3 " pdb=" O5 BMA G 3 " pdb=" C5 BMA G 3 " ideal model delta sigma weight residual 118.82 113.57 5.25 3.00e+00 1.11e-01 3.06e+00 angle pdb=" C1 BMA H 3 " pdb=" O5 BMA H 3 " pdb=" C5 BMA H 3 " ideal model delta sigma weight residual 118.82 113.58 5.24 3.00e+00 1.11e-01 3.05e+00 angle pdb=" C1 BMA I 3 " pdb=" O5 BMA I 3 " pdb=" C5 BMA I 3 " ideal model delta sigma weight residual 118.82 113.70 5.12 3.00e+00 1.11e-01 2.92e+00 angle pdb=" CA TYR D 66 " pdb=" CB TYR D 66 " pdb=" CG TYR D 66 " ideal model delta sigma weight residual 113.90 116.88 -2.98 1.80e+00 3.09e-01 2.74e+00 ... (remaining 23590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 10320 23.65 - 47.30: 110 47.30 - 70.94: 8 70.94 - 94.59: 29 94.59 - 118.24: 34 Dihedral angle restraints: 10501 sinusoidal: 4495 harmonic: 6006 Sorted by residual: dihedral pdb=" N1 EPE D 501 " pdb=" C5 EPE D 501 " pdb=" C6 EPE D 501 " pdb=" N4 EPE D 501 " ideal model delta sinusoidal sigma weight residual -58.50 59.74 -118.24 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C2 EPE C 501 " pdb=" C6 EPE C 501 " pdb=" N1 EPE C 501 " pdb=" C5 EPE C 501 " ideal model delta sinusoidal sigma weight residual 58.85 -59.32 118.17 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" N1 EPE B 501 " pdb=" C5 EPE B 501 " pdb=" C6 EPE B 501 " pdb=" N4 EPE B 501 " ideal model delta sinusoidal sigma weight residual -58.50 59.53 -118.03 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 10498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2281 0.053 - 0.106: 344 0.106 - 0.158: 58 0.158 - 0.211: 7 0.211 - 0.264: 5 Chirality restraints: 2695 Sorted by residual: chirality pdb=" C1 MAN F 5 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 2.23e+01 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.01e+01 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.75e+01 ... (remaining 2692 not shown) Planarity restraints: 2905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " -0.028 2.00e-02 2.50e+03 2.33e-02 6.77e+00 pdb=" C7 NAG E 501 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " 0.038 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E 256 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO E 257 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO E 257 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 257 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 435 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO E 436 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 436 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 436 " 0.019 5.00e-02 4.00e+02 ... (remaining 2902 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1270 2.74 - 3.28: 16430 3.28 - 3.82: 29002 3.82 - 4.36: 36407 4.36 - 4.90: 61157 Nonbonded interactions: 144266 Sorted by model distance: nonbonded pdb=" ND2AASN A 41 " pdb=" O ARG A 169 " model vdw 2.205 2.520 nonbonded pdb=" OH TYR E 171 " pdb=" OH TYR E 250 " model vdw 2.209 2.440 nonbonded pdb=" OD2 ASP A 146 " pdb=" NE2 GLN A 148 " model vdw 2.324 2.520 nonbonded pdb=" OD2 ASP B 146 " pdb=" NE2 GLN B 148 " model vdw 2.324 2.520 nonbonded pdb=" OD2 ASP D 146 " pdb=" NE2 GLN D 148 " model vdw 2.325 2.520 ... (remaining 144261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) selection = (chain 'B' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) selection = (chain 'C' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) selection = (chain 'D' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 425 or resid 427 through 447)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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=0.50 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.180 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 53.720 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.180 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:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.003 0.038 17300 Z= 0.171 Angle : 0.459 5.591 23595 Z= 0.212 Chirality : 0.042 0.264 2695 Planarity : 0.003 0.059 2896 Dihedral : 12.100 118.241 6661 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.39 % Allowed : 2.47 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 2.50 (0.20), residues: 2027 helix: 2.53 (0.21), residues: 583 sheet: 1.62 (0.22), residues: 644 loop : 1.17 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 426 HIS 0.001 0.000 HIS C 191 PHE 0.006 0.001 PHE E 115 TYR 0.015 0.001 TYR D 66 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 543 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.7908 (p90) cc_final: 0.7419 (p90) REVERT: A 277 TYR cc_start: 0.8246 (p90) cc_final: 0.8009 (p90) REVERT: A 306 PHE cc_start: 0.7443 (t80) cc_final: 0.6816 (t80) REVERT: A 433 PHE cc_start: 0.7807 (t80) cc_final: 0.7474 (t80) REVERT: B 304 TYR cc_start: 0.8608 (t80) cc_final: 0.8388 (t80) REVERT: C 141 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7651 (mtt-85) REVERT: C 274 LYS cc_start: 0.8012 (mttt) cc_final: 0.7778 (mptt) REVERT: C 434 THR cc_start: 0.9243 (m) cc_final: 0.8932 (p) REVERT: D 227 MET cc_start: 0.7140 (mmt) cc_final: 0.6633 (mmm) REVERT: D 243 ASN cc_start: 0.8072 (t0) cc_final: 0.7854 (t0) REVERT: D 271 THR cc_start: 0.8687 (p) cc_final: 0.8476 (p) REVERT: E 244 ARG cc_start: 0.7753 (ttt-90) cc_final: 0.7531 (ttt-90) REVERT: E 310 LEU cc_start: 0.8476 (tp) cc_final: 0.8247 (tp) REVERT: E 330 PHE cc_start: 0.7626 (t80) cc_final: 0.7324 (t80) REVERT: K 468 LEU cc_start: 0.7718 (tp) cc_final: 0.7017 (tp) REVERT: K 495 TYR cc_start: 0.8360 (m-80) cc_final: 0.8007 (m-80) REVERT: L 407 LEU cc_start: 0.8228 (mt) cc_final: 0.7938 (mm) REVERT: L 472 ASN cc_start: 0.8035 (t0) cc_final: 0.7714 (t0) outliers start: 6 outliers final: 1 residues processed: 548 average time/residue: 1.2462 time to fit residues: 760.8218 Evaluate side-chains 350 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 349 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 103 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 148 GLN C 185 GLN D 439 ASN E 147 GLN E 200 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17300 Z= 0.308 Angle : 0.650 8.735 23595 Z= 0.331 Chirality : 0.046 0.205 2695 Planarity : 0.004 0.060 2896 Dihedral : 12.205 115.954 2931 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.43 % Allowed : 15.38 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 2.12 (0.19), residues: 2027 helix: 2.42 (0.21), residues: 566 sheet: 1.44 (0.21), residues: 627 loop : 0.77 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 237 HIS 0.005 0.001 HIS B 107 PHE 0.024 0.002 PHE D 301 TYR 0.021 0.002 TYR D 299 ARG 0.010 0.001 ARG M 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 359 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8989 (ptt) cc_final: 0.8692 (ptt) REVERT: A 90 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: A 244 TYR cc_start: 0.7891 (p90) cc_final: 0.7425 (p90) REVERT: A 306 PHE cc_start: 0.7695 (t80) cc_final: 0.7124 (t80) REVERT: B 279 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7393 (mttt) REVERT: C 21 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8202 (mptt) REVERT: C 141 ARG cc_start: 0.8133 (mtt90) cc_final: 0.7886 (mtt-85) REVERT: C 235 LEU cc_start: 0.8758 (tp) cc_final: 0.8528 (tt) REVERT: C 274 LYS cc_start: 0.8123 (mttt) cc_final: 0.7873 (mmmm) REVERT: C 434 THR cc_start: 0.9161 (m) cc_final: 0.8881 (p) REVERT: D 9 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7026 (ptt) REVERT: D 243 ASN cc_start: 0.8192 (t0) cc_final: 0.7856 (t0) REVERT: D 274 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8297 (mmmm) REVERT: D 294 LEU cc_start: 0.8943 (mt) cc_final: 0.8608 (mp) REVERT: E 260 LEU cc_start: 0.8601 (pp) cc_final: 0.8313 (mm) REVERT: E 330 PHE cc_start: 0.7742 (t80) cc_final: 0.7346 (t80) REVERT: K 407 LEU cc_start: 0.8183 (mt) cc_final: 0.7869 (mp) REVERT: K 470 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7573 (mpp) REVERT: L 3 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8269 (mp10) outliers start: 76 outliers final: 30 residues processed: 389 average time/residue: 1.1496 time to fit residues: 504.6178 Evaluate side-chains 363 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 328 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain E residue 445 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 450 SER Chi-restraints excluded: chain M residue 452 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 chunk 178 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN A C 185 GLN E 147 GLN E 210 GLN E 213 GLN K 472 ASN M 414 HIS M 464 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17300 Z= 0.171 Angle : 0.571 9.560 23595 Z= 0.286 Chirality : 0.044 0.203 2695 Planarity : 0.004 0.069 2896 Dihedral : 11.905 112.042 2929 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.70 % Allowed : 17.62 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 2.05 (0.19), residues: 2027 helix: 2.39 (0.21), residues: 566 sheet: 1.31 (0.21), residues: 632 loop : 0.80 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 237 HIS 0.002 0.001 HIS A 267 PHE 0.024 0.001 PHE A 433 TYR 0.022 0.001 TYR D 299 ARG 0.007 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 344 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8525 (mtpp) cc_final: 0.7914 (mttp) REVERT: A 90 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: A 141 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7700 (mpt180) REVERT: A 244 TYR cc_start: 0.7904 (p90) cc_final: 0.7397 (p90) REVERT: A 277 TYR cc_start: 0.8160 (p90) cc_final: 0.7952 (p90) REVERT: A 306 PHE cc_start: 0.7657 (t80) cc_final: 0.7015 (t80) REVERT: B 265 ASN cc_start: 0.8157 (t0) cc_final: 0.7941 (t0) REVERT: B 279 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7482 (mttt) REVERT: C 61 MET cc_start: 0.9014 (ptt) cc_final: 0.8694 (ptt) REVERT: C 225 THR cc_start: 0.8592 (p) cc_final: 0.8382 (t) REVERT: C 235 LEU cc_start: 0.8687 (tp) cc_final: 0.8453 (tt) REVERT: C 244 TYR cc_start: 0.7526 (p90) cc_final: 0.7267 (p90) REVERT: C 274 LYS cc_start: 0.8089 (mttt) cc_final: 0.7845 (mmmm) REVERT: C 434 THR cc_start: 0.9151 (m) cc_final: 0.8852 (p) REVERT: D 9 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7054 (ptt) REVERT: D 227 MET cc_start: 0.7415 (mmm) cc_final: 0.7122 (mmp) REVERT: D 243 ASN cc_start: 0.8275 (t0) cc_final: 0.7939 (t0) REVERT: D 274 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8242 (mmmm) REVERT: D 306 PHE cc_start: 0.7746 (t80) cc_final: 0.7109 (t80) REVERT: E 107 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: E 330 PHE cc_start: 0.7755 (t80) cc_final: 0.7360 (t80) REVERT: K 407 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7932 (mp) REVERT: K 470 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7767 (mpp) REVERT: L 3 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8346 (mp10) REVERT: L 472 ASN cc_start: 0.7464 (t0) cc_final: 0.7228 (t0) REVERT: M 454 ARG cc_start: 0.7281 (mtm110) cc_final: 0.6968 (mtp180) outliers start: 62 outliers final: 24 residues processed: 367 average time/residue: 1.1679 time to fit residues: 482.8384 Evaluate side-chains 355 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 324 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 407 LEU Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain M residue 452 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 189 optimal weight: 0.0870 chunk 93 optimal weight: 0.0470 chunk 169 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 185 GLN A 224 GLN B 41 ASN A C 185 GLN E 147 GLN E 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17300 Z= 0.329 Angle : 0.653 10.786 23595 Z= 0.325 Chirality : 0.048 0.703 2695 Planarity : 0.004 0.064 2896 Dihedral : 11.654 116.387 2929 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.83 % Allowed : 17.40 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.70 (0.19), residues: 2027 helix: 2.06 (0.21), residues: 579 sheet: 1.16 (0.21), residues: 630 loop : 0.54 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 440 HIS 0.008 0.001 HIS E 104 PHE 0.023 0.002 PHE A 433 TYR 0.023 0.002 TYR D 299 ARG 0.004 0.001 ARG E 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 339 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8319 (mmtm) REVERT: A 141 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7658 (mpt180) REVERT: A 244 TYR cc_start: 0.7989 (p90) cc_final: 0.7489 (p90) REVERT: A 306 PHE cc_start: 0.7701 (t80) cc_final: 0.7169 (t80) REVERT: A 426 TRP cc_start: 0.7673 (m-90) cc_final: 0.7197 (m-10) REVERT: C 21 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8293 (mptt) REVERT: C 61 MET cc_start: 0.9011 (ptt) cc_final: 0.8713 (ptt) REVERT: C 235 LEU cc_start: 0.8724 (tp) cc_final: 0.8514 (tt) REVERT: C 274 LYS cc_start: 0.8156 (mttt) cc_final: 0.7834 (mmmm) REVERT: C 305 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8142 (mp) REVERT: C 434 THR cc_start: 0.9135 (m) cc_final: 0.8842 (p) REVERT: D 18 LYS cc_start: 0.8386 (tttt) cc_final: 0.8057 (ttpt) REVERT: D 87 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.8949 (p) REVERT: D 192 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7861 (mtt-85) REVERT: D 243 ASN cc_start: 0.8269 (t0) cc_final: 0.7874 (t0) REVERT: D 274 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8387 (mmmm) REVERT: D 306 PHE cc_start: 0.7826 (t80) cc_final: 0.7214 (t80) REVERT: E 43 ASN cc_start: 0.6360 (OUTLIER) cc_final: 0.6135 (p0) REVERT: E 208 LYS cc_start: 0.8720 (mttm) cc_final: 0.8434 (mtpt) REVERT: E 330 PHE cc_start: 0.7814 (t80) cc_final: 0.7440 (t80) REVERT: K 3 GLN cc_start: 0.8198 (mp10) cc_final: 0.7991 (mp10) REVERT: K 407 LEU cc_start: 0.8343 (mt) cc_final: 0.8084 (mp) REVERT: K 469 GLU cc_start: 0.8085 (mp0) cc_final: 0.7883 (mp0) REVERT: L 472 ASN cc_start: 0.7752 (t0) cc_final: 0.7551 (t0) REVERT: M 454 ARG cc_start: 0.7348 (mtm110) cc_final: 0.7036 (mtp180) outliers start: 81 outliers final: 39 residues processed: 372 average time/residue: 1.1693 time to fit residues: 490.5424 Evaluate side-chains 361 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 317 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 456 THR Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 497 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 0.0060 chunk 141 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 170 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN E 147 GLN E 213 GLN K 471 ASN L 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17300 Z= 0.155 Angle : 0.584 11.010 23595 Z= 0.289 Chirality : 0.045 0.554 2695 Planarity : 0.003 0.063 2896 Dihedral : 11.298 112.372 2929 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.82 % Allowed : 19.36 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.79 (0.19), residues: 2027 helix: 2.16 (0.21), residues: 573 sheet: 1.31 (0.21), residues: 617 loop : 0.51 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 237 HIS 0.002 0.001 HIS E 240 PHE 0.026 0.001 PHE A 433 TYR 0.022 0.001 TYR C 299 ARG 0.005 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 341 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8683 (mtpp) cc_final: 0.8268 (mmtm) REVERT: A 244 TYR cc_start: 0.7958 (p90) cc_final: 0.7444 (p90) REVERT: A 306 PHE cc_start: 0.7695 (t80) cc_final: 0.7108 (t80) REVERT: A 426 TRP cc_start: 0.7652 (m-90) cc_final: 0.7191 (m-10) REVERT: C 21 LYS cc_start: 0.8597 (mmmm) cc_final: 0.8338 (mptt) REVERT: C 61 MET cc_start: 0.8994 (ptt) cc_final: 0.8784 (ptt) REVERT: C 235 LEU cc_start: 0.8727 (tp) cc_final: 0.8525 (tt) REVERT: C 305 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8099 (mp) REVERT: C 434 THR cc_start: 0.9136 (m) cc_final: 0.8844 (p) REVERT: D 9 MET cc_start: 0.7464 (ttp) cc_final: 0.7075 (ptt) REVERT: D 218 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6644 (mm) REVERT: D 243 ASN cc_start: 0.8290 (t0) cc_final: 0.7887 (t0) REVERT: D 274 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8279 (mmmm) REVERT: D 306 PHE cc_start: 0.7829 (t80) cc_final: 0.7339 (t80) REVERT: E 43 ASN cc_start: 0.6385 (OUTLIER) cc_final: 0.6158 (p0) REVERT: E 208 LYS cc_start: 0.8679 (mttm) cc_final: 0.8422 (mtpt) REVERT: E 330 PHE cc_start: 0.7758 (t80) cc_final: 0.7428 (t80) REVERT: K 3 GLN cc_start: 0.8189 (mp10) cc_final: 0.7985 (mp10) REVERT: K 407 LEU cc_start: 0.8219 (mt) cc_final: 0.7939 (mp) REVERT: K 456 THR cc_start: 0.8066 (t) cc_final: 0.7841 (t) REVERT: K 469 GLU cc_start: 0.8055 (mp0) cc_final: 0.7726 (mp0) REVERT: L 472 ASN cc_start: 0.7765 (t0) cc_final: 0.7564 (t0) REVERT: M 408 SER cc_start: 0.8099 (t) cc_final: 0.7215 (p) REVERT: M 454 ARG cc_start: 0.7325 (mtm110) cc_final: 0.7057 (mtp180) outliers start: 63 outliers final: 26 residues processed: 370 average time/residue: 1.1597 time to fit residues: 483.3280 Evaluate side-chains 338 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 308 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 189 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 224 GLN E 147 GLN K 471 ASN K 472 ASN M 464 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17300 Z= 0.415 Angle : 0.694 13.154 23595 Z= 0.346 Chirality : 0.049 0.483 2695 Planarity : 0.004 0.061 2896 Dihedral : 11.275 119.588 2929 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.55 % Allowed : 18.74 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.42 (0.19), residues: 2027 helix: 1.87 (0.21), residues: 578 sheet: 0.97 (0.21), residues: 629 loop : 0.37 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 440 HIS 0.005 0.001 HIS B 267 PHE 0.027 0.002 PHE A 433 TYR 0.024 0.002 TYR C 299 ARG 0.005 0.001 ARG E 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 326 time to evaluate : 1.964 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8118 (mttp) REVERT: A 21 LYS cc_start: 0.7993 (mptm) cc_final: 0.7708 (mmmm) REVERT: A 141 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7277 (mtt180) REVERT: A 244 TYR cc_start: 0.8016 (p90) cc_final: 0.7537 (p90) REVERT: A 277 TYR cc_start: 0.8173 (p90) cc_final: 0.7907 (p90) REVERT: A 306 PHE cc_start: 0.7695 (t80) cc_final: 0.7245 (t80) REVERT: A 426 TRP cc_start: 0.7736 (m-90) cc_final: 0.7209 (m-10) REVERT: B 40 MET cc_start: 0.8735 (mtt) cc_final: 0.8511 (mtt) REVERT: C 61 MET cc_start: 0.9030 (ptt) cc_final: 0.8720 (ptt) REVERT: C 235 LEU cc_start: 0.8823 (tp) cc_final: 0.8601 (tt) REVERT: C 305 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8213 (mp) REVERT: C 434 THR cc_start: 0.9150 (m) cc_final: 0.8863 (p) REVERT: D 9 MET cc_start: 0.7487 (ttp) cc_final: 0.7215 (ptp) REVERT: D 55 MET cc_start: 0.8909 (tpp) cc_final: 0.8216 (mmm) REVERT: D 141 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7519 (mtt-85) REVERT: D 243 ASN cc_start: 0.8285 (t0) cc_final: 0.7845 (t0) REVERT: D 274 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8428 (mmmm) REVERT: D 306 PHE cc_start: 0.8034 (t80) cc_final: 0.7455 (t80) REVERT: E 43 ASN cc_start: 0.6688 (OUTLIER) cc_final: 0.6457 (p0) REVERT: E 208 LYS cc_start: 0.8703 (mttm) cc_final: 0.8445 (mtpt) REVERT: K 407 LEU cc_start: 0.8288 (mt) cc_final: 0.8028 (mp) REVERT: K 469 GLU cc_start: 0.8199 (mp0) cc_final: 0.7914 (mp0) REVERT: L 452 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8311 (ttpp) REVERT: L 507 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: M 408 SER cc_start: 0.8167 (t) cc_final: 0.7318 (p) REVERT: M 473 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8551 (mm) outliers start: 75 outliers final: 44 residues processed: 357 average time/residue: 1.0779 time to fit residues: 438.2953 Evaluate side-chains 359 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 307 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 452 LYS Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain L residue 507 GLN Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 461 ASN Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 473 LEU Chi-restraints excluded: chain M residue 477 ASP Chi-restraints excluded: chain M residue 497 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN E 147 GLN E 213 GLN K 471 ASN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17300 Z= 0.189 Angle : 0.609 11.870 23595 Z= 0.301 Chirality : 0.045 0.432 2695 Planarity : 0.003 0.060 2896 Dihedral : 10.044 117.549 2929 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.54 % Allowed : 20.76 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.59 (0.19), residues: 2027 helix: 2.07 (0.21), residues: 568 sheet: 1.02 (0.21), residues: 625 loop : 0.49 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 237 HIS 0.003 0.001 HIS E 240 PHE 0.026 0.001 PHE A 433 TYR 0.023 0.001 TYR C 299 ARG 0.005 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 325 time to evaluate : 1.956 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8090 (mttp) REVERT: A 244 TYR cc_start: 0.7980 (p90) cc_final: 0.7754 (p90) REVERT: A 277 TYR cc_start: 0.8075 (p90) cc_final: 0.7822 (p90) REVERT: A 426 TRP cc_start: 0.7746 (m-90) cc_final: 0.7246 (m-10) REVERT: B 61 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8776 (ptt) REVERT: C 235 LEU cc_start: 0.8799 (tp) cc_final: 0.8586 (tt) REVERT: C 305 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8127 (mp) REVERT: C 434 THR cc_start: 0.9126 (m) cc_final: 0.8848 (p) REVERT: D 9 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7168 (ptp) REVERT: D 215 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8468 (ttpp) REVERT: D 243 ASN cc_start: 0.8248 (t0) cc_final: 0.7822 (t0) REVERT: D 274 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8352 (mmmm) REVERT: D 306 PHE cc_start: 0.8021 (t80) cc_final: 0.7531 (t80) REVERT: E 43 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.6408 (p0) REVERT: E 173 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7941 (mpp) REVERT: E 208 LYS cc_start: 0.8705 (mttm) cc_final: 0.8444 (mtpt) REVERT: K 407 LEU cc_start: 0.8223 (mt) cc_final: 0.7993 (mp) REVERT: K 456 THR cc_start: 0.8042 (t) cc_final: 0.7680 (t) REVERT: K 469 GLU cc_start: 0.8138 (mp0) cc_final: 0.7823 (mp0) REVERT: K 470 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7418 (mpt) REVERT: M 408 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7320 (p) REVERT: M 473 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8505 (mm) outliers start: 56 outliers final: 26 residues processed: 346 average time/residue: 1.0598 time to fit residues: 417.7418 Evaluate side-chains 356 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 320 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 473 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 224 GLN C 64 GLN E 147 GLN K 426 GLN K 471 ASN M 464 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17300 Z= 0.263 Angle : 0.630 12.721 23595 Z= 0.313 Chirality : 0.046 0.419 2695 Planarity : 0.004 0.059 2896 Dihedral : 9.614 114.620 2929 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.54 % Allowed : 21.21 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.53 (0.19), residues: 2027 helix: 1.95 (0.21), residues: 578 sheet: 1.02 (0.21), residues: 623 loop : 0.46 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 237 HIS 0.003 0.001 HIS B 267 PHE 0.029 0.002 PHE A 433 TYR 0.024 0.002 TYR C 299 ARG 0.004 0.000 ARG M 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 324 time to evaluate : 2.021 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.6749 (mmm) cc_final: 0.6431 (tpt) REVERT: A 13 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8072 (mttp) REVERT: A 21 LYS cc_start: 0.8105 (mmtm) cc_final: 0.7751 (mmmm) REVERT: A 277 TYR cc_start: 0.8083 (p90) cc_final: 0.7740 (p90) REVERT: A 426 TRP cc_start: 0.7743 (m-90) cc_final: 0.7245 (m-10) REVERT: C 61 MET cc_start: 0.8999 (ptt) cc_final: 0.8797 (ptt) REVERT: C 235 LEU cc_start: 0.8799 (tp) cc_final: 0.8590 (tt) REVERT: C 244 TYR cc_start: 0.7946 (p90) cc_final: 0.7542 (p90) REVERT: C 274 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7701 (ttmm) REVERT: C 305 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8129 (mp) REVERT: C 306 PHE cc_start: 0.6797 (t80) cc_final: 0.6506 (t80) REVERT: C 434 THR cc_start: 0.9144 (m) cc_final: 0.8860 (p) REVERT: D 9 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7194 (ptp) REVERT: D 215 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8480 (ttpp) REVERT: D 243 ASN cc_start: 0.8254 (t0) cc_final: 0.7827 (t0) REVERT: D 274 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8397 (mmmm) REVERT: D 306 PHE cc_start: 0.8037 (t80) cc_final: 0.7546 (t80) REVERT: E 43 ASN cc_start: 0.6701 (OUTLIER) cc_final: 0.6493 (p0) REVERT: E 208 LYS cc_start: 0.8670 (mttm) cc_final: 0.8413 (mtpt) REVERT: K 469 GLU cc_start: 0.8145 (mp0) cc_final: 0.7816 (mp0) REVERT: K 470 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7351 (mpt) REVERT: K 474 LYS cc_start: 0.7310 (mtmm) cc_final: 0.7055 (mptp) REVERT: M 408 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7386 (p) REVERT: M 504 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7523 (mp10) outliers start: 56 outliers final: 36 residues processed: 350 average time/residue: 1.0298 time to fit residues: 411.4650 Evaluate side-chains 351 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 308 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 477 ASP Chi-restraints excluded: chain M residue 497 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 105 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN E 147 GLN K 426 GLN K 471 ASN M 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17300 Z= 0.199 Angle : 0.612 12.782 23595 Z= 0.302 Chirality : 0.045 0.391 2695 Planarity : 0.003 0.059 2896 Dihedral : 9.316 112.781 2929 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.37 % Allowed : 21.89 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.60 (0.19), residues: 2027 helix: 2.03 (0.21), residues: 572 sheet: 0.98 (0.21), residues: 625 loop : 0.56 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 237 HIS 0.004 0.001 HIS D 267 PHE 0.029 0.001 PHE A 433 TYR 0.022 0.002 TYR C 299 ARG 0.004 0.000 ARG K 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 324 time to evaluate : 1.951 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.6713 (mmm) cc_final: 0.6336 (tpt) REVERT: A 13 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8003 (mttp) REVERT: A 21 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7840 (mmmm) REVERT: A 277 TYR cc_start: 0.7943 (p90) cc_final: 0.7547 (p90) REVERT: A 426 TRP cc_start: 0.7775 (m-90) cc_final: 0.7281 (m-10) REVERT: C 49 MET cc_start: 0.7447 (tmm) cc_final: 0.7203 (pp-130) REVERT: C 235 LEU cc_start: 0.8788 (tp) cc_final: 0.8579 (tt) REVERT: C 274 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7749 (ttmm) REVERT: C 434 THR cc_start: 0.9143 (m) cc_final: 0.8863 (p) REVERT: D 9 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7176 (ptp) REVERT: D 215 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: D 243 ASN cc_start: 0.8252 (t0) cc_final: 0.7844 (t0) REVERT: D 274 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8361 (mmmm) REVERT: D 306 PHE cc_start: 0.8053 (t80) cc_final: 0.7551 (t80) REVERT: E 173 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8022 (mpp) REVERT: E 208 LYS cc_start: 0.8668 (mttm) cc_final: 0.8421 (mtpt) REVERT: K 469 GLU cc_start: 0.8012 (mp0) cc_final: 0.7787 (mp0) REVERT: K 474 LYS cc_start: 0.7333 (mtmm) cc_final: 0.7079 (mttp) REVERT: K 504 GLN cc_start: 0.8180 (mp10) cc_final: 0.7680 (pm20) REVERT: M 408 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7396 (p) REVERT: M 466 VAL cc_start: 0.8218 (t) cc_final: 0.7910 (p) REVERT: M 504 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7532 (mp10) outliers start: 53 outliers final: 34 residues processed: 347 average time/residue: 1.0429 time to fit residues: 415.3592 Evaluate side-chains 351 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 312 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 461 ASN Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 477 ASP Chi-restraints excluded: chain M residue 497 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9980 chunk 186 optimal weight: 0.1980 chunk 113 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN C 64 GLN E 147 GLN K 426 GLN K 471 ASN M 464 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17300 Z= 0.169 Angle : 0.615 13.372 23595 Z= 0.302 Chirality : 0.045 0.387 2695 Planarity : 0.003 0.059 2896 Dihedral : 9.064 112.368 2929 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.58 % Allowed : 22.84 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.65 (0.19), residues: 2027 helix: 2.02 (0.22), residues: 572 sheet: 1.07 (0.21), residues: 619 loop : 0.59 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 237 HIS 0.003 0.000 HIS E 240 PHE 0.091 0.002 PHE A 301 TYR 0.028 0.001 TYR A 299 ARG 0.004 0.000 ARG A 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 320 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6715 (mmm) cc_final: 0.6407 (tpt) REVERT: A 13 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8030 (mttp) REVERT: A 21 LYS cc_start: 0.8181 (mmtm) cc_final: 0.7825 (mmmm) REVERT: A 277 TYR cc_start: 0.7919 (p90) cc_final: 0.7545 (p90) REVERT: A 426 TRP cc_start: 0.7780 (m-90) cc_final: 0.7283 (m-10) REVERT: C 49 MET cc_start: 0.7505 (tmm) cc_final: 0.7275 (pp-130) REVERT: C 235 LEU cc_start: 0.8767 (tp) cc_final: 0.8544 (tt) REVERT: C 434 THR cc_start: 0.9145 (m) cc_final: 0.8866 (p) REVERT: D 9 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7200 (ptp) REVERT: D 182 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7553 (mp0) REVERT: D 215 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: D 243 ASN cc_start: 0.8243 (t0) cc_final: 0.7866 (t0) REVERT: D 274 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8349 (mmmm) REVERT: D 306 PHE cc_start: 0.8054 (t80) cc_final: 0.7554 (t80) REVERT: E 173 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8002 (mpp) REVERT: E 208 LYS cc_start: 0.8653 (mttm) cc_final: 0.8420 (mtpt) REVERT: K 469 GLU cc_start: 0.8021 (mp0) cc_final: 0.7780 (mp0) REVERT: K 474 LYS cc_start: 0.7280 (mtmm) cc_final: 0.7009 (mttp) REVERT: K 504 GLN cc_start: 0.8200 (mp10) cc_final: 0.7683 (pm20) REVERT: L 463 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8202 (mtmm) REVERT: M 466 VAL cc_start: 0.8228 (t) cc_final: 0.7890 (p) REVERT: M 504 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7541 (mp10) outliers start: 39 outliers final: 25 residues processed: 337 average time/residue: 1.0473 time to fit residues: 402.7140 Evaluate side-chains 344 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 315 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 452 LYS Chi-restraints excluded: chain M residue 461 ASN Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN C 64 GLN E 147 GLN K 471 ASN M 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.073257 restraints weight = 164571.396| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 5.12 r_work: 0.2663 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17300 Z= 0.263 Angle : 0.645 13.701 23595 Z= 0.317 Chirality : 0.046 0.381 2695 Planarity : 0.004 0.059 2896 Dihedral : 9.202 114.367 2929 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.53 % Allowed : 22.95 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.25 % 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: 1.63 (0.19), residues: 2027 helix: 1.85 (0.21), residues: 600 sheet: 1.00 (0.21), residues: 621 loop : 0.71 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 237 HIS 0.002 0.001 HIS B 267 PHE 0.030 0.002 PHE A 433 TYR 0.023 0.002 TYR E 318 ARG 0.004 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7620.58 seconds wall clock time: 136 minutes 57.95 seconds (8217.95 seconds total)