Starting phenix.real_space_refine (version: dev) on Sat May 14 05:00:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/05_2022/7qn6_14068_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/05_2022/7qn6_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_14068/05_2022/7qn6_14068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/05_2022/7qn6_14068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/05_2022/7qn6_14068_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn6_14068/05_2022/7qn6_14068_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A 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-4597/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: {'PTRANS': 12, 'CIS': 1, 'TRANS': 312, 'PCIS': 1} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'CIS': 1, 'TRANS': 312, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 1, 'TRANS': 312, 'PCIS': 1} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'CIS': 1, 'TRANS': 312, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 1, 'TRANS': 312, 'PCIS': 1} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'CIS': 1, 'TRANS': 312, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 1, 'TRANS': 312, 'PCIS': 1} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'CIS': 1, 'TRANS': 312, 'PCIS': 1} 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: {'PTRANS': 11, 'CIS': 1, 'TRANS': 310, 'PCIS': 1} 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 chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 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 chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 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 chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 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 chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 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 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: 14.10, per 1000 atoms: 0.84 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: 6.84 Conformation dependent library (CDL) restraints added in 3.6 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: 1.66 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: 5.61 Time building geometry restraints manager: 7.37 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=" C3 MAN F 5 " pdb=" C2 MAN F 5 " pdb=" O2 MAN F 5 " ideal model delta sigma weight residual 105.65 110.08 -4.43 2.47e+00 1.64e-01 3.23e+00 angle pdb=" C3 MAN I 4 " pdb=" C2 MAN I 4 " pdb=" O2 MAN I 4 " ideal model delta sigma weight residual 105.65 110.05 -4.40 2.47e+00 1.64e-01 3.19e+00 angle pdb=" C3 MAN H 4 " pdb=" C2 MAN H 4 " pdb=" O2 MAN H 4 " ideal model delta sigma weight residual 105.65 110.05 -4.40 2.47e+00 1.64e-01 3.18e+00 angle pdb=" C3 MAN F 4 " pdb=" C2 MAN F 4 " pdb=" O2 MAN F 4 " ideal model delta sigma weight residual 105.65 110.04 -4.39 2.47e+00 1.64e-01 3.16e+00 angle pdb=" C3 MAN H 5 " pdb=" C2 MAN H 5 " pdb=" O2 MAN H 5 " ideal model delta sigma weight residual 105.65 110.03 -4.38 2.47e+00 1.64e-01 3.16e+00 ... (remaining 23590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 10004 23.65 - 47.30: 102 47.30 - 70.94: 2 70.94 - 94.59: 9 94.59 - 118.24: 15 Dihedral angle restraints: 10132 sinusoidal: 4126 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 10129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2143 0.045 - 0.090: 364 0.090 - 0.135: 180 0.135 - 0.180: 3 0.180 - 0.225: 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 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. 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: 1.460 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: 0.020 Extract box with map and model: 6.920 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.130 Process input model: 51.030 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 : 0.002 0.038 17300 Z= 0.127 Angle : 0.413 5.591 23595 Z= 0.205 Chirality : 0.041 0.225 2695 Planarity : 0.003 0.059 2896 Dihedral : 9.959 118.241 6292 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 0.39 % 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 *********************** 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 : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 548 average time/residue: 1.1581 time to fit residues: 711.4880 Evaluate side-chains 340 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 339 time to evaluate : 1.930 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2789 time to fit residues: 2.9423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 82 optimal weight: 0.6980 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: 2.3184 ------------------------------------------------------------------------------- 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: 0.8772 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 17300 Z= 0.306 Angle : 0.648 8.858 23595 Z= 0.333 Chirality : 0.045 0.179 2695 Planarity : 0.005 0.082 2896 Dihedral : 9.596 119.200 2560 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 4.60 % 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: 2.11 (0.19), residues: 2027 helix: 2.44 (0.21), residues: 566 sheet: 1.37 (0.21), residues: 632 loop : 0.81 (0.23), residues: 829 *********************** 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 430 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 351 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 32 residues processed: 384 average time/residue: 0.9939 time to fit residues: 435.8231 Evaluate side-chains 341 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 309 time to evaluate : 1.936 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 19 average time/residue: 0.5013 time to fit residues: 14.5986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0060 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 192 optimal weight: 0.0040 chunk 158 optimal weight: 0.6980 chunk 176 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 overall best weight: 0.5410 ------------------------------------------------------------------------------- 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** A 185 GLN B 41 ASN A C 185 GLN D 243 ASN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 17300 Z= 0.154 Angle : 0.560 9.369 23595 Z= 0.283 Chirality : 0.042 0.193 2695 Planarity : 0.004 0.065 2896 Dihedral : 9.453 113.887 2560 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 3.98 % 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: 2.06 (0.19), residues: 2027 helix: 2.36 (0.21), residues: 564 sheet: 1.43 (0.21), residues: 623 loop : 0.75 (0.23), residues: 840 *********************** 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 409 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 342 time to evaluate : 1.905 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 23 residues processed: 371 average time/residue: 0.9986 time to fit residues: 422.9460 Evaluate side-chains 328 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 305 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 7 average time/residue: 0.6680 time to fit residues: 8.0813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 189 optimal weight: 0.0870 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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 C 224 GLN D 439 ASN E 147 GLN E 213 GLN L 426 GLN M 464 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 17300 Z= 0.380 Angle : 0.650 10.020 23595 Z= 0.330 Chirality : 0.046 0.215 2695 Planarity : 0.004 0.065 2896 Dihedral : 9.585 117.862 2560 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 4.43 % 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: 2.01 (0.21), residues: 579 sheet: 1.18 (0.21), residues: 625 loop : 0.46 (0.22), residues: 823 *********************** 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 392 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 318 time to evaluate : 1.975 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 43 residues processed: 356 average time/residue: 1.0569 time to fit residues: 429.7465 Evaluate side-chains 341 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 298 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 25 residues processed: 22 average time/residue: 0.4254 time to fit residues: 15.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 0.0010 chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN C 265 ASN E 147 GLN E 213 GLN K 471 ASN L 504 GLN M 464 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 17300 Z= 0.205 Angle : 0.600 12.058 23595 Z= 0.301 Chirality : 0.047 0.918 2695 Planarity : 0.003 0.063 2896 Dihedral : 9.360 113.602 2560 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 4.10 % 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: 1.66 (0.19), residues: 2027 helix: 1.99 (0.21), residues: 579 sheet: 1.19 (0.21), residues: 621 loop : 0.50 (0.22), residues: 827 *********************** 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 394 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 326 time to evaluate : 1.945 Fit side-chains outliers start: 68 outliers final: 40 residues processed: 359 average time/residue: 0.9776 time to fit residues: 403.3549 Evaluate side-chains 351 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 311 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 26 residues processed: 17 average time/residue: 0.5672 time to fit residues: 14.5082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN C 224 GLN C 265 ASN D 439 ASN E 147 GLN E 213 GLN K 471 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 17300 Z= 0.387 Angle : 0.682 11.424 23595 Z= 0.344 Chirality : 0.047 0.617 2695 Planarity : 0.004 0.061 2896 Dihedral : 9.100 119.120 2560 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 4.55 % 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: 1.41 (0.19), residues: 2027 helix: 1.91 (0.21), residues: 574 sheet: 0.94 (0.21), residues: 629 loop : 0.34 (0.22), residues: 824 *********************** 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: 74 poor density : 327 time to evaluate : 1.795 Fit side-chains outliers start: 74 outliers final: 46 residues processed: 362 average time/residue: 0.9629 time to fit residues: 403.1027 Evaluate side-chains 357 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 311 time to evaluate : 1.947 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 28 residues processed: 21 average time/residue: 0.4509 time to fit residues: 15.0458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 118 optimal weight: 0.0970 chunk 115 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 185 GLN C 224 GLN C 265 ASN E 147 GLN E 213 GLN K 471 ASN M 464 ASN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17300 Z= 0.185 Angle : 0.602 10.729 23595 Z= 0.302 Chirality : 0.044 0.520 2695 Planarity : 0.004 0.092 2896 Dihedral : 7.985 112.974 2560 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 3.48 % 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: 1.56 (0.19), residues: 2027 helix: 1.98 (0.21), residues: 573 sheet: 0.98 (0.21), residues: 629 loop : 0.54 (0.23), residues: 825 *********************** 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 377 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 322 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 33 residues processed: 350 average time/residue: 0.9539 time to fit residues: 384.7335 Evaluate side-chains 344 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 311 time to evaluate : 1.891 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 11 average time/residue: 0.7652 time to fit residues: 12.5395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN E 147 GLN E 213 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 17300 Z= 0.265 Angle : 0.625 12.726 23595 Z= 0.315 Chirality : 0.045 0.438 2695 Planarity : 0.004 0.060 2896 Dihedral : 7.932 115.286 2560 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 2.97 % 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: 1.47 (0.19), residues: 2027 helix: 1.88 (0.22), residues: 575 sheet: 0.98 (0.21), residues: 629 loop : 0.45 (0.22), residues: 823 *********************** 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 374 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 328 time to evaluate : 1.899 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 35 residues processed: 355 average time/residue: 0.9765 time to fit residues: 396.7899 Evaluate side-chains 353 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 318 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 25 residues processed: 12 average time/residue: 0.5600 time to fit residues: 10.8193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 3.9990 chunk 180 optimal weight: 0.4980 chunk 165 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 105 optimal weight: 0.0970 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 159 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN C 265 ASN E 147 GLN E 213 GLN M 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17300 Z= 0.199 Angle : 0.599 12.835 23595 Z= 0.302 Chirality : 0.044 0.341 2695 Planarity : 0.003 0.060 2896 Dihedral : 7.810 112.661 2560 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 2.97 % 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: 1.57 (0.19), residues: 2027 helix: 1.93 (0.22), residues: 573 sheet: 0.98 (0.21), residues: 629 loop : 0.59 (0.23), residues: 825 *********************** 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 381 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 335 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 31 residues processed: 362 average time/residue: 1.0632 time to fit residues: 440.0907 Evaluate side-chains 348 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 317 time to evaluate : 1.920 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 25 residues processed: 9 average time/residue: 0.4868 time to fit residues: 8.1379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 113 optimal weight: 0.0070 chunk 88 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- 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 E 213 GLN K 426 GLN M 464 ASN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 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 : 0.003 0.046 17300 Z= 0.186 Angle : 0.608 13.364 23595 Z= 0.304 Chirality : 0.044 0.353 2695 Planarity : 0.003 0.060 2896 Dihedral : 7.720 113.310 2560 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 2.36 % 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: 1.58 (0.19), residues: 2027 helix: 1.86 (0.21), residues: 572 sheet: 1.09 (0.21), residues: 623 loop : 0.57 (0.23), residues: 832 ********************** 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 364 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 329 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 29 residues processed: 351 average time/residue: 0.9946 time to fit residues: 400.3427 Evaluate side-chains 350 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 321 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 7 average time/residue: 0.4487 time to fit residues: 6.4440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 65 optimal weight: 0.0980 chunk 159 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 E 213 GLN K 471 ASN ** K 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 504 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.111056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.073373 restraints weight = 163563.636| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 5.06 r_work: 0.2822 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work: 0.2765 rms_B_bonded: 4.57 restraints_weight: 0.1250 r_work: 0.2737 rms_B_bonded: 4.70 restraints_weight: 0.0625 r_work: 0.2707 rms_B_bonded: 4.91 restraints_weight: 0.0312 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 17300 Z= 0.272 Angle : 0.629 13.325 23595 Z= 0.318 Chirality : 0.045 0.373 2695 Planarity : 0.004 0.060 2896 Dihedral : 7.876 114.915 2560 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 2.64 % 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: 1.50 (0.19), residues: 2027 helix: 1.87 (0.22), residues: 569 sheet: 1.01 (0.21), residues: 621 loop : 0.51 (0.22), residues: 837 =============================================================================== Job complete usr+sys time: 6590.11 seconds wall clock time: 117 minutes 33.96 seconds (7053.96 seconds total)