Starting phenix.real_space_refine on Fri Feb 16 23:22:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnd_14075/02_2024/7qnd_14075_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnd_14075/02_2024/7qnd_14075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnd_14075/02_2024/7qnd_14075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnd_14075/02_2024/7qnd_14075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnd_14075/02_2024/7qnd_14075_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qnd_14075/02_2024/7qnd_14075_updated.pdb" } resolution = 3.4 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 89 5.16 5 C 10938 2.51 5 N 2705 2.21 5 O 3078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16810 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2744 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: 2689 Chain: "B" 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: 2662 Chain: "C" Number of atoms: 2760 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: 2669 Chain: "D" Number of atoms: 2725 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: 2710 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'HSM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'EI7': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 12 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 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: 13.74, per 1000 atoms: 0.82 Number of scatterers: 16810 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 89 16.00 O 3078 8.00 N 2705 7.00 C 10938 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 502 " - " 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: 7.20 Conformation dependent library (CDL) restraints added in 4.8 seconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3814 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 29 sheets defined 31.7% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 8 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: 3.547A 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: 3.646A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.633A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.592A 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: 3.637A 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 8 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: 3.547A 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: 3.646A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.633A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.592A 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: 3.637A 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 8 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: 3.547A 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: 3.646A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.633A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.592A 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: 3.637A 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 8 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: 3.547A 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: 3.647A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.633A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.592A 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: 3.638A 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: 3.771A 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 Proline residue: E 257 - end of helix removed outlier: 4.046A 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: 4.098A 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 removed outlier: 3.517A pdb=" N LEU E 325 " --> pdb=" O VAL E 321 " (cutoff:3.500A) 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: 6.272A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.465A 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: 4.044A 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: 3.821A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.889A 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: 6.687A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 7.036A 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: 6.273A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.465A 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: 4.044A 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: 3.821A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.888A 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: 6.687A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.039A 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: 6.272A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.465A 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: 4.044A 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: 3.822A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.888A 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: 6.687A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.036A 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: 6.272A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.465A 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: 4.044A 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: 3.821A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.888A 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: 6.687A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.038A 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: 6.201A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.745A 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: 4.005A 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: 5.678A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 175 through 178 Processing sheet with id= T, first strand: chain 'E' and resid 129 through 134 removed outlier: 6.793A pdb=" N THR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA E 132 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR E 159 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 2 through 7 Processing sheet with id= V, first strand: chain 'K' and resid 506 through 508 removed outlier: 3.707A pdb=" N VAL K 508 " --> pdb=" O ALA K 479 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL K 480 " --> pdb=" O GLN K 426 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG K 425 " --> pdb=" O PHE K 434 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE K 434 " --> pdb=" O ARG K 425 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 484 through 486 removed outlier: 3.867A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 2 through 7 Processing sheet with id= Y, first strand: chain 'L' and resid 506 through 508 removed outlier: 3.707A pdb=" N VAL L 508 " --> pdb=" O ALA L 479 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL L 480 " --> pdb=" O GLN L 426 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 484 through 486 removed outlier: 3.867A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 2 through 7 Processing sheet with id= AB, first strand: chain 'M' and resid 506 through 508 removed outlier: 3.706A pdb=" N VAL M 508 " --> pdb=" O ALA M 479 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL M 480 " --> pdb=" O GLN M 426 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 484 through 486 removed outlier: 3.867A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 2156 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: 5.58 Time building geometry restraints manager: 7.58 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: 5110 1.34 - 1.46: 4432 1.46 - 1.58: 7596 1.58 - 1.69: 0 1.69 - 1.81: 153 Bond restraints: 17291 Sorted by residual: bond pdb=" N EI7 E 501 " pdb=" C EI7 E 501 " ideal model delta sigma weight residual 1.388 1.457 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C EI7 E 501 " pdb=" C2 EI7 E 501 " ideal model delta sigma weight residual 1.446 1.477 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 MAN I 5 " pdb=" O5 MAN I 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 17286 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.10: 501 107.10 - 113.84: 9780 113.84 - 120.58: 6715 120.58 - 127.32: 6381 127.32 - 134.06: 200 Bond angle restraints: 23577 Sorted by residual: angle pdb=" N EI7 E 501 " pdb=" C EI7 E 501 " pdb=" O EI7 E 501 " ideal model delta sigma weight residual 124.11 130.30 -6.19 3.00e+00 1.11e-01 4.25e+00 angle pdb=" CA ATYR D 66 " pdb=" CB ATYR D 66 " pdb=" CG ATYR D 66 " ideal model delta sigma weight residual 113.90 117.21 -3.31 1.80e+00 3.09e-01 3.39e+00 angle pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " pdb=" C5 BMA F 3 " ideal model delta sigma weight residual 118.82 113.40 5.42 3.00e+00 1.11e-01 3.27e+00 angle pdb=" C1 BMA H 3 " pdb=" O5 BMA H 3 " pdb=" C5 BMA H 3 " ideal model delta sigma weight residual 118.82 113.44 5.38 3.00e+00 1.11e-01 3.21e+00 angle pdb=" C1 BMA G 3 " pdb=" O5 BMA G 3 " pdb=" C5 BMA G 3 " ideal model delta sigma weight residual 118.82 113.51 5.31 3.00e+00 1.11e-01 3.13e+00 ... (remaining 23572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 10283 21.14 - 42.29: 144 42.29 - 63.43: 14 63.43 - 84.57: 31 84.57 - 105.72: 16 Dihedral angle restraints: 10488 sinusoidal: 4484 harmonic: 6004 Sorted by residual: dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.01 105.72 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.71 105.42 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.50 105.21 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 10485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2269 0.052 - 0.105: 358 0.105 - 0.157: 51 0.157 - 0.210: 9 0.210 - 0.262: 4 Chirality restraints: 2691 Sorted by residual: 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 -2.29 -0.11 2.00e-02 2.50e+03 2.88e+01 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 2.30 0.10 2.00e-02 2.50e+03 2.71e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.02e+01 ... (remaining 2688 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 435 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO E 436 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 436 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 436 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 171 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO E 172 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 172 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 172 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ATYR D 66 " 0.009 2.00e-02 2.50e+03 6.80e-03 9.24e-01 pdb=" CG ATYR D 66 " -0.016 2.00e-02 2.50e+03 pdb=" CD1ATYR D 66 " 0.003 2.00e-02 2.50e+03 pdb=" CD2ATYR D 66 " -0.000 2.00e-02 2.50e+03 pdb=" CE1ATYR D 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE2ATYR D 66 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ATYR D 66 " -0.000 2.00e-02 2.50e+03 pdb=" OH ATYR D 66 " 0.000 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1499 2.75 - 3.29: 16440 3.29 - 3.82: 28976 3.82 - 4.36: 35798 4.36 - 4.90: 60658 Nonbonded interactions: 143371 Sorted by model distance: nonbonded pdb=" OH TYR E 171 " pdb=" OH TYR E 250 " model vdw 2.210 2.440 nonbonded pdb=" ND2AASN A 41 " pdb=" O ARG A 169 " model vdw 2.249 2.520 nonbonded pdb=" ND2AASN B 41 " pdb=" O ARG B 169 " model vdw 2.312 2.520 nonbonded pdb=" ND2AASN C 41 " pdb=" O ARG C 169 " model vdw 2.318 2.520 nonbonded pdb=" OD2 ASP C 146 " pdb=" NE2 GLN C 148 " model vdw 2.337 2.520 ... (remaining 143366 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 425 or resid 427 thro \ ugh 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 425 or resid 427 thro \ ugh 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 425 or resid 427 thro \ ugh 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 425 or resid 427 thro \ ugh 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: 0.990 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: 6.090 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 54.660 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 0.069 17291 Z= 0.173 Angle : 0.458 6.187 23577 Z= 0.208 Chirality : 0.042 0.262 2691 Planarity : 0.003 0.033 2900 Dihedral : 10.267 105.716 6650 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.45 % Allowed : 1.68 % Favored : 97.87 % 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: 2.54 (0.20), residues: 2024 helix: 2.97 (0.21), residues: 553 sheet: 1.52 (0.22), residues: 656 loop : 1.04 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 67 HIS 0.001 0.000 HIS E 104 PHE 0.007 0.001 PHE E 90 TYR 0.008 0.001 TYR B 126 ARG 0.001 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 602 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6735 (mtp) cc_final: 0.6044 (mpp) REVERT: A 85 ASN cc_start: 0.7088 (p0) cc_final: 0.6872 (p0) REVERT: A 151 THR cc_start: 0.8574 (p) cc_final: 0.8265 (p) REVERT: A 192 ARG cc_start: 0.7490 (mtt180) cc_final: 0.6943 (mtt180) REVERT: A 229 SER cc_start: 0.9333 (m) cc_final: 0.9055 (t) REVERT: A 268 LEU cc_start: 0.8589 (tp) cc_final: 0.8358 (tp) REVERT: A 284 TYR cc_start: 0.8394 (t80) cc_final: 0.8192 (t80) REVERT: A 288 CYS cc_start: 0.9209 (m) cc_final: 0.8728 (m) REVERT: A 429 ILE cc_start: 0.9032 (tp) cc_final: 0.8701 (mm) REVERT: B 298 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 301 PHE cc_start: 0.8107 (t80) cc_final: 0.7888 (t80) REVERT: B 433 PHE cc_start: 0.8830 (t80) cc_final: 0.8599 (t80) REVERT: C 52 GLU cc_start: 0.8018 (mp0) cc_final: 0.7728 (mm-30) REVERT: C 95 ASP cc_start: 0.8348 (p0) cc_final: 0.8131 (p0) REVERT: C 138 MET cc_start: 0.8699 (mtt) cc_final: 0.8001 (mtt) REVERT: C 141 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7665 (mtm-85) REVERT: C 243 ASN cc_start: 0.7510 (t0) cc_final: 0.6833 (p0) REVERT: C 250 ARG cc_start: 0.8430 (mtp180) cc_final: 0.8166 (mtp180) REVERT: C 274 LYS cc_start: 0.8927 (mttt) cc_final: 0.8713 (mtmt) REVERT: D 223 LEU cc_start: 0.8990 (mt) cc_final: 0.8477 (pp) REVERT: D 227 MET cc_start: 0.8341 (mmt) cc_final: 0.8076 (tpp) REVERT: D 243 ASN cc_start: 0.7359 (t0) cc_final: 0.6726 (t0) REVERT: D 268 LEU cc_start: 0.8021 (tp) cc_final: 0.7417 (tp) REVERT: D 270 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7917 (mm-30) REVERT: D 306 PHE cc_start: 0.7943 (t80) cc_final: 0.7024 (t80) REVERT: D 425 ARG cc_start: 0.8963 (ttt180) cc_final: 0.8709 (ttm170) REVERT: D 437 LEU cc_start: 0.9187 (tp) cc_final: 0.8971 (mm) REVERT: E 142 LYS cc_start: 0.8951 (mttt) cc_final: 0.8568 (mttm) REVERT: E 222 THR cc_start: 0.8717 (m) cc_final: 0.8456 (p) REVERT: E 290 MET cc_start: 0.8589 (tpp) cc_final: 0.8121 (tmm) REVERT: E 317 CYS cc_start: 0.9008 (m) cc_final: 0.8804 (m) REVERT: E 332 HIS cc_start: 0.8807 (t70) cc_final: 0.8590 (t70) REVERT: K 460 ASP cc_start: 0.7492 (p0) cc_final: 0.7200 (p0) REVERT: K 509 THR cc_start: 0.8012 (m) cc_final: 0.7448 (p) REVERT: L 459 ARG cc_start: 0.8121 (pmt-80) cc_final: 0.7488 (ppt170) REVERT: L 460 ASP cc_start: 0.7239 (p0) cc_final: 0.6835 (p0) REVERT: L 474 LYS cc_start: 0.8873 (mttt) cc_final: 0.8639 (ttpt) REVERT: L 501 TYR cc_start: 0.8355 (m-80) cc_final: 0.7982 (m-80) REVERT: M 455 PHE cc_start: 0.7613 (m-10) cc_final: 0.7008 (m-10) REVERT: M 464 ASN cc_start: 0.8391 (m-40) cc_final: 0.8188 (m-40) REVERT: M 465 THR cc_start: 0.8517 (m) cc_final: 0.8302 (p) REVERT: M 481 TYR cc_start: 0.8538 (m-80) cc_final: 0.8010 (m-10) REVERT: M 482 TYR cc_start: 0.8024 (m-80) cc_final: 0.7756 (m-80) REVERT: M 509 THR cc_start: 0.8695 (m) cc_final: 0.8367 (t) outliers start: 8 outliers final: 0 residues processed: 608 average time/residue: 0.3203 time to fit residues: 278.4419 Evaluate side-chains 375 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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: 7.9990 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN C 265 ASN E 147 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 504 GLN M 507 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17291 Z= 0.326 Angle : 0.699 14.672 23577 Z= 0.350 Chirality : 0.046 0.224 2691 Planarity : 0.004 0.045 2900 Dihedral : 9.007 78.998 2920 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.92 % Allowed : 13.03 % Favored : 84.05 % 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: 1.93 (0.19), residues: 2024 helix: 2.41 (0.21), residues: 565 sheet: 1.16 (0.21), residues: 642 loop : 0.69 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 315 HIS 0.004 0.001 HIS C 107 PHE 0.023 0.002 PHE A 221 TYR 0.027 0.002 TYR D 284 ARG 0.007 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 388 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6714 (mtp) cc_final: 0.5999 (mpp) REVERT: A 66 TYR cc_start: 0.7148 (m-80) cc_final: 0.6907 (m-80) REVERT: A 192 ARG cc_start: 0.7191 (mtt180) cc_final: 0.6935 (mtp85) REVERT: A 429 ILE cc_start: 0.8975 (tp) cc_final: 0.8675 (mm) REVERT: B 55 MET cc_start: 0.8705 (mmm) cc_final: 0.8426 (mmt) REVERT: B 433 PHE cc_start: 0.8883 (t80) cc_final: 0.8642 (t80) REVERT: C 18 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8587 (ptpp) REVERT: C 141 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7904 (mtm-85) REVERT: C 226 TYR cc_start: 0.8979 (m-80) cc_final: 0.8764 (m-80) REVERT: C 243 ASN cc_start: 0.7532 (t0) cc_final: 0.7006 (p0) REVERT: C 277 TYR cc_start: 0.8262 (p90) cc_final: 0.7556 (p90) REVERT: D 13 LYS cc_start: 0.9217 (tttt) cc_final: 0.8973 (tppt) REVERT: D 18 LYS cc_start: 0.9110 (mtmm) cc_final: 0.8772 (mtmm) REVERT: D 147 GLU cc_start: 0.7776 (tp30) cc_final: 0.7432 (tp30) REVERT: D 220 TYR cc_start: 0.8413 (t80) cc_final: 0.8105 (t80) REVERT: D 223 LEU cc_start: 0.8956 (mt) cc_final: 0.8505 (pp) REVERT: D 227 MET cc_start: 0.8516 (mmt) cc_final: 0.8269 (tpp) REVERT: D 243 ASN cc_start: 0.7407 (t0) cc_final: 0.7017 (t0) REVERT: D 425 ARG cc_start: 0.8939 (ttt180) cc_final: 0.8672 (ttm170) REVERT: E 222 THR cc_start: 0.8839 (m) cc_final: 0.8594 (p) REVERT: E 253 GLN cc_start: 0.8037 (tp40) cc_final: 0.7817 (tp40) REVERT: M 3 GLN cc_start: 0.7843 (mp10) cc_final: 0.7639 (mp10) REVERT: M 431 GLU cc_start: 0.8111 (tp30) cc_final: 0.7544 (tm-30) REVERT: M 482 TYR cc_start: 0.8284 (m-80) cc_final: 0.7802 (m-80) outliers start: 52 outliers final: 32 residues processed: 414 average time/residue: 0.2874 time to fit residues: 178.1399 Evaluate side-chains 386 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 353 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 454 ARG Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 507 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 414 HIS M 472 ASN ** M 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17291 Z= 0.190 Angle : 0.609 11.976 23577 Z= 0.304 Chirality : 0.044 0.203 2691 Planarity : 0.003 0.055 2900 Dihedral : 8.603 75.014 2920 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.02 % Allowed : 14.99 % Favored : 82.99 % 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: 1.75 (0.19), residues: 2024 helix: 2.24 (0.21), residues: 565 sheet: 0.98 (0.21), residues: 651 loop : 0.68 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 237 HIS 0.002 0.001 HIS K 414 PHE 0.014 0.001 PHE L 455 TYR 0.023 0.002 TYR M 481 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 361 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6800 (mtp) cc_final: 0.6115 (mpp) REVERT: A 66 TYR cc_start: 0.7219 (m-80) cc_final: 0.6937 (m-80) REVERT: A 192 ARG cc_start: 0.7255 (mtt180) cc_final: 0.7004 (mtp85) REVERT: A 429 ILE cc_start: 0.8965 (tp) cc_final: 0.8661 (mm) REVERT: B 55 MET cc_start: 0.8683 (mmm) cc_final: 0.8156 (mmm) REVERT: B 286 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7371 (ttp) REVERT: B 433 PHE cc_start: 0.8798 (t80) cc_final: 0.8590 (t80) REVERT: C 18 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8512 (ptpp) REVERT: C 55 MET cc_start: 0.9014 (tpp) cc_final: 0.8288 (mmt) REVERT: C 141 ARG cc_start: 0.8108 (mtt90) cc_final: 0.7816 (mtm-85) REVERT: C 298 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8230 (tm-30) REVERT: D 13 LYS cc_start: 0.9163 (tttt) cc_final: 0.8878 (tptt) REVERT: D 223 LEU cc_start: 0.8934 (mt) cc_final: 0.8540 (pp) REVERT: D 226 TYR cc_start: 0.8847 (m-80) cc_final: 0.8602 (m-10) REVERT: D 227 MET cc_start: 0.8495 (mmt) cc_final: 0.8228 (tpp) REVERT: D 243 ASN cc_start: 0.7422 (t0) cc_final: 0.6808 (t0) REVERT: D 270 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7123 (mm-30) REVERT: D 284 TYR cc_start: 0.9030 (t80) cc_final: 0.8798 (t80) REVERT: E 222 THR cc_start: 0.8815 (m) cc_final: 0.8610 (p) REVERT: E 253 GLN cc_start: 0.8138 (tp40) cc_final: 0.7866 (tp40) REVERT: K 449 ASP cc_start: 0.8901 (p0) cc_final: 0.8580 (p0) REVERT: M 3 GLN cc_start: 0.7844 (mp10) cc_final: 0.7637 (mp10) REVERT: M 431 GLU cc_start: 0.7998 (tp30) cc_final: 0.7544 (tm-30) REVERT: M 469 GLU cc_start: 0.8025 (mp0) cc_final: 0.7592 (mp0) REVERT: M 474 LYS cc_start: 0.8996 (mttt) cc_final: 0.8725 (mtmm) REVERT: M 481 TYR cc_start: 0.8307 (m-10) cc_final: 0.7878 (m-10) REVERT: M 482 TYR cc_start: 0.8354 (m-80) cc_final: 0.7953 (m-80) outliers start: 34 outliers final: 24 residues processed: 377 average time/residue: 0.2817 time to fit residues: 159.3385 Evaluate side-chains 356 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 330 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 472 ASN 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: 1.9990 chunk 92 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 507 GLN L 414 HIS ** L 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17291 Z= 0.221 Angle : 0.600 11.157 23577 Z= 0.299 Chirality : 0.044 0.302 2691 Planarity : 0.003 0.042 2900 Dihedral : 8.157 70.295 2920 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.81 % Allowed : 15.22 % Favored : 81.98 % 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: 1.65 (0.19), residues: 2024 helix: 2.13 (0.21), residues: 563 sheet: 1.00 (0.21), residues: 624 loop : 0.58 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 237 HIS 0.003 0.001 HIS C 267 PHE 0.014 0.001 PHE D 289 TYR 0.021 0.002 TYR B 299 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 344 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6738 (mtp) cc_final: 0.6101 (mpp) REVERT: A 66 TYR cc_start: 0.7281 (m-80) cc_final: 0.7013 (m-80) REVERT: A 227 MET cc_start: 0.8169 (ttt) cc_final: 0.7850 (ttp) REVERT: A 294 LEU cc_start: 0.8753 (mp) cc_final: 0.8534 (mp) REVERT: A 429 ILE cc_start: 0.8975 (tp) cc_final: 0.8667 (mm) REVERT: A 445 TYR cc_start: 0.7985 (t80) cc_final: 0.7640 (t80) REVERT: B 55 MET cc_start: 0.8736 (mmm) cc_final: 0.8238 (mmm) REVERT: B 286 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7359 (ttp) REVERT: B 433 PHE cc_start: 0.8863 (t80) cc_final: 0.8642 (t80) REVERT: C 18 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8575 (ptpp) REVERT: C 52 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7463 (mm-30) REVERT: C 138 MET cc_start: 0.8616 (mtt) cc_final: 0.8387 (mtt) REVERT: C 141 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7847 (mtm-85) REVERT: C 298 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8300 (tm-30) REVERT: D 13 LYS cc_start: 0.9128 (tttt) cc_final: 0.8829 (tptt) REVERT: D 18 LYS cc_start: 0.9000 (mtmm) cc_final: 0.8675 (mtmm) REVERT: D 223 LEU cc_start: 0.8956 (mt) cc_final: 0.8577 (pp) REVERT: D 227 MET cc_start: 0.8559 (mmt) cc_final: 0.8247 (tpp) REVERT: E 170 LYS cc_start: 0.8278 (mttt) cc_final: 0.7708 (mmmt) REVERT: E 222 THR cc_start: 0.8804 (m) cc_final: 0.8565 (p) REVERT: E 253 GLN cc_start: 0.8161 (tp40) cc_final: 0.7860 (tp40) REVERT: K 449 ASP cc_start: 0.8985 (p0) cc_final: 0.8670 (p0) REVERT: K 481 TYR cc_start: 0.7369 (m-80) cc_final: 0.7037 (m-80) REVERT: M 3 GLN cc_start: 0.7890 (mp10) cc_final: 0.7673 (mp10) REVERT: M 472 ASN cc_start: 0.8941 (t0) cc_final: 0.8695 (t0) REVERT: M 477 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: M 481 TYR cc_start: 0.8371 (m-10) cc_final: 0.8160 (m-10) REVERT: M 482 TYR cc_start: 0.8404 (m-80) cc_final: 0.8037 (m-80) outliers start: 46 outliers final: 32 residues processed: 366 average time/residue: 0.2845 time to fit residues: 156.9204 Evaluate side-chains 367 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 332 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 259 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 509 THR Chi-restraints excluded: chain L residue 467 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17291 Z= 0.325 Angle : 0.628 11.062 23577 Z= 0.315 Chirality : 0.045 0.231 2691 Planarity : 0.003 0.032 2900 Dihedral : 8.023 68.424 2920 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.82 % Allowed : 14.94 % Favored : 81.25 % 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: 1.31 (0.19), residues: 2024 helix: 1.75 (0.21), residues: 591 sheet: 0.95 (0.21), residues: 582 loop : 0.30 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 237 HIS 0.010 0.001 HIS E 240 PHE 0.015 0.002 PHE D 98 TYR 0.024 0.002 TYR B 299 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 329 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6697 (mtp) cc_final: 0.6088 (mpp) REVERT: A 66 TYR cc_start: 0.7352 (m-80) cc_final: 0.7072 (m-80) REVERT: A 227 MET cc_start: 0.8207 (ttt) cc_final: 0.7944 (ttp) REVERT: A 294 LEU cc_start: 0.8784 (mp) cc_final: 0.8542 (mp) REVERT: A 429 ILE cc_start: 0.9014 (tp) cc_final: 0.8697 (mm) REVERT: A 445 TYR cc_start: 0.8030 (t80) cc_final: 0.7709 (t80) REVERT: B 55 MET cc_start: 0.8889 (mmm) cc_final: 0.8642 (mmt) REVERT: B 433 PHE cc_start: 0.8890 (t80) cc_final: 0.8664 (t80) REVERT: C 18 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8724 (pttm) REVERT: C 52 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7426 (mm-30) REVERT: C 55 MET cc_start: 0.8998 (tpp) cc_final: 0.8767 (tpp) REVERT: C 138 MET cc_start: 0.8736 (mtt) cc_final: 0.8163 (mtt) REVERT: C 141 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7941 (mtm-85) REVERT: C 298 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8422 (tm-30) REVERT: D 13 LYS cc_start: 0.9148 (tttt) cc_final: 0.8835 (tptt) REVERT: D 18 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8678 (mtmm) REVERT: D 223 LEU cc_start: 0.8969 (mt) cc_final: 0.8597 (pp) REVERT: D 227 MET cc_start: 0.8615 (mmt) cc_final: 0.8287 (tpp) REVERT: D 243 ASN cc_start: 0.7598 (t0) cc_final: 0.7047 (t0) REVERT: E 83 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8004 (mmm) REVERT: E 170 LYS cc_start: 0.8370 (mttt) cc_final: 0.7830 (mmmt) REVERT: E 177 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: E 222 THR cc_start: 0.8693 (m) cc_final: 0.8404 (p) REVERT: E 253 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7926 (tp40) REVERT: E 290 MET cc_start: 0.8628 (mmm) cc_final: 0.8315 (tpt) REVERT: E 333 PHE cc_start: 0.8555 (t80) cc_final: 0.7847 (t80) REVERT: K 449 ASP cc_start: 0.9097 (p0) cc_final: 0.8802 (p0) REVERT: K 481 TYR cc_start: 0.7511 (m-80) cc_final: 0.7235 (m-80) REVERT: M 3 GLN cc_start: 0.7981 (mp10) cc_final: 0.7741 (mp10) REVERT: M 4 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8645 (mt) REVERT: M 421 MET cc_start: 0.8763 (mmm) cc_final: 0.8223 (mmm) REVERT: M 477 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: M 482 TYR cc_start: 0.8476 (m-80) cc_final: 0.8049 (m-80) outliers start: 63 outliers final: 41 residues processed: 363 average time/residue: 0.2716 time to fit residues: 150.1867 Evaluate side-chains 362 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 315 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 259 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 L residue 467 TYR Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 464 ASN Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 477 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17291 Z= 0.371 Angle : 0.652 10.877 23577 Z= 0.327 Chirality : 0.046 0.239 2691 Planarity : 0.003 0.032 2900 Dihedral : 7.940 67.661 2920 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.15 % Allowed : 14.99 % Favored : 80.85 % 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: 1.17 (0.18), residues: 2024 helix: 1.65 (0.21), residues: 591 sheet: 1.04 (0.22), residues: 548 loop : 0.09 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 237 HIS 0.005 0.001 HIS B 107 PHE 0.017 0.002 PHE D 98 TYR 0.026 0.002 TYR C 220 ARG 0.004 0.001 ARG D 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 317 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6720 (mtp) cc_final: 0.6112 (mpp) REVERT: A 66 TYR cc_start: 0.7376 (m-80) cc_final: 0.7119 (m-80) REVERT: A 227 MET cc_start: 0.8272 (ttt) cc_final: 0.7985 (ttp) REVERT: A 429 ILE cc_start: 0.9023 (tp) cc_final: 0.8712 (mm) REVERT: A 445 TYR cc_start: 0.8070 (t80) cc_final: 0.7700 (t80) REVERT: B 433 PHE cc_start: 0.8910 (t80) cc_final: 0.8683 (t80) REVERT: C 18 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8733 (pttm) REVERT: C 52 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7506 (mm-30) REVERT: C 138 MET cc_start: 0.8727 (mtt) cc_final: 0.8412 (mtt) REVERT: C 141 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7987 (mtm-85) REVERT: D 223 LEU cc_start: 0.8875 (mt) cc_final: 0.8547 (pp) REVERT: D 227 MET cc_start: 0.8609 (mmt) cc_final: 0.8278 (tpp) REVERT: D 243 ASN cc_start: 0.7605 (t0) cc_final: 0.7054 (t0) REVERT: E 83 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7961 (mmm) REVERT: E 128 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8641 (p0) REVERT: E 170 LYS cc_start: 0.8438 (mttt) cc_final: 0.7994 (mmmt) REVERT: E 177 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: E 179 MET cc_start: 0.7696 (mmm) cc_final: 0.7172 (mmm) REVERT: E 253 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7974 (tp40) REVERT: E 290 MET cc_start: 0.8582 (mmm) cc_final: 0.8332 (tpt) REVERT: E 333 PHE cc_start: 0.8564 (t80) cc_final: 0.7864 (t80) REVERT: K 1 GLN cc_start: 0.8223 (pm20) cc_final: 0.8022 (pm20) REVERT: K 482 TYR cc_start: 0.8269 (m-10) cc_final: 0.7954 (m-10) REVERT: L 504 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: M 3 GLN cc_start: 0.7991 (mp10) cc_final: 0.7739 (mp10) REVERT: M 4 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8644 (mt) REVERT: M 421 MET cc_start: 0.8767 (mmm) cc_final: 0.8252 (mmm) REVERT: M 431 GLU cc_start: 0.8193 (tp30) cc_final: 0.7546 (tm-30) REVERT: M 482 TYR cc_start: 0.8493 (m-80) cc_final: 0.7776 (m-10) outliers start: 69 outliers final: 48 residues processed: 353 average time/residue: 0.2624 time to fit residues: 141.9951 Evaluate side-chains 363 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 308 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 415 THR Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 509 THR Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 464 ASN Chi-restraints excluded: chain M residue 467 TYR 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: 6.9990 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 138 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 507 GLN L 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17291 Z= 0.180 Angle : 0.607 11.394 23577 Z= 0.298 Chirality : 0.044 0.233 2691 Planarity : 0.003 0.033 2900 Dihedral : 7.385 62.594 2920 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.64 % Allowed : 16.62 % Favored : 80.74 % 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: 1.15 (0.19), residues: 2024 helix: 1.64 (0.21), residues: 591 sheet: 0.95 (0.22), residues: 559 loop : 0.14 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 237 HIS 0.003 0.000 HIS E 240 PHE 0.016 0.001 PHE A 289 TYR 0.022 0.001 TYR B 299 ARG 0.003 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 327 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6603 (mtp) cc_final: 0.6078 (mpp) REVERT: A 66 TYR cc_start: 0.7299 (m-80) cc_final: 0.7043 (m-80) REVERT: A 227 MET cc_start: 0.8250 (ttt) cc_final: 0.7960 (ttp) REVERT: A 429 ILE cc_start: 0.8998 (tp) cc_final: 0.8689 (mm) REVERT: A 445 TYR cc_start: 0.8063 (t80) cc_final: 0.7772 (t80) REVERT: B 55 MET cc_start: 0.8791 (mmt) cc_final: 0.8483 (mmt) REVERT: B 433 PHE cc_start: 0.8838 (t80) cc_final: 0.8634 (t80) REVERT: C 18 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8774 (pttm) REVERT: C 52 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7494 (mm-30) REVERT: C 138 MET cc_start: 0.8756 (mtt) cc_final: 0.8394 (mtt) REVERT: C 226 TYR cc_start: 0.9105 (m-80) cc_final: 0.8819 (m-80) REVERT: C 298 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8345 (tm-30) REVERT: D 223 LEU cc_start: 0.8835 (mt) cc_final: 0.8431 (pp) REVERT: D 227 MET cc_start: 0.8588 (mmt) cc_final: 0.8255 (tpp) REVERT: D 243 ASN cc_start: 0.7550 (t0) cc_final: 0.7013 (t0) REVERT: E 83 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7954 (mmm) REVERT: E 128 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8583 (p0) REVERT: E 170 LYS cc_start: 0.8321 (mttt) cc_final: 0.7806 (mmmt) REVERT: E 179 MET cc_start: 0.7668 (mmm) cc_final: 0.7154 (mmm) REVERT: E 222 THR cc_start: 0.8728 (m) cc_final: 0.8477 (p) REVERT: E 253 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8000 (tp40) REVERT: E 290 MET cc_start: 0.8572 (mmm) cc_final: 0.8362 (tpt) REVERT: K 469 GLU cc_start: 0.7412 (mp0) cc_final: 0.6842 (mp0) REVERT: K 482 TYR cc_start: 0.8236 (m-10) cc_final: 0.7881 (m-10) REVERT: M 3 GLN cc_start: 0.8055 (mp10) cc_final: 0.7809 (mp10) REVERT: M 4 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8654 (mt) REVERT: M 482 TYR cc_start: 0.8470 (m-80) cc_final: 0.8041 (m-80) outliers start: 42 outliers final: 32 residues processed: 348 average time/residue: 0.2777 time to fit residues: 146.5251 Evaluate side-chains 349 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 312 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 509 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 17 optimal weight: 0.0770 chunk 148 optimal weight: 9.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 ASN L 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17291 Z= 0.187 Angle : 0.609 10.794 23577 Z= 0.298 Chirality : 0.044 0.238 2691 Planarity : 0.003 0.074 2900 Dihedral : 7.101 59.972 2920 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.86 % Allowed : 17.07 % Favored : 80.07 % 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: 1.19 (0.19), residues: 2024 helix: 1.65 (0.21), residues: 591 sheet: 0.99 (0.22), residues: 559 loop : 0.16 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 237 HIS 0.003 0.001 HIS E 240 PHE 0.020 0.001 PHE A 289 TYR 0.022 0.001 TYR B 299 ARG 0.003 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 322 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6559 (mtp) cc_final: 0.6068 (mpp) REVERT: A 66 TYR cc_start: 0.7306 (m-80) cc_final: 0.7096 (m-80) REVERT: A 227 MET cc_start: 0.8275 (ttt) cc_final: 0.7887 (ttp) REVERT: A 429 ILE cc_start: 0.9001 (tp) cc_final: 0.8690 (mm) REVERT: A 445 TYR cc_start: 0.8082 (t80) cc_final: 0.7784 (t80) REVERT: B 55 MET cc_start: 0.8776 (mmt) cc_final: 0.8484 (mmt) REVERT: B 286 MET cc_start: 0.7853 (ttt) cc_final: 0.7411 (tmm) REVERT: C 18 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8804 (pttm) REVERT: C 52 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7499 (mm-30) REVERT: C 138 MET cc_start: 0.8697 (mtt) cc_final: 0.8353 (mtt) REVERT: C 298 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8368 (tm-30) REVERT: D 180 ARG cc_start: 0.7340 (mmp80) cc_final: 0.6958 (mmp80) REVERT: D 227 MET cc_start: 0.8592 (mmt) cc_final: 0.8264 (tpp) REVERT: D 243 ASN cc_start: 0.7539 (t0) cc_final: 0.7015 (t0) REVERT: D 244 TYR cc_start: 0.7963 (p90) cc_final: 0.7729 (p90) REVERT: E 83 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8008 (mmm) REVERT: E 128 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8578 (p0) REVERT: E 170 LYS cc_start: 0.8319 (mttt) cc_final: 0.7796 (mmmt) REVERT: E 179 MET cc_start: 0.7650 (mmm) cc_final: 0.7119 (mmm) REVERT: E 222 THR cc_start: 0.8756 (m) cc_final: 0.8522 (p) REVERT: E 253 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8013 (tp40) REVERT: E 290 MET cc_start: 0.8579 (mmm) cc_final: 0.8362 (tpt) REVERT: K 469 GLU cc_start: 0.7439 (mp0) cc_final: 0.6810 (mp0) REVERT: K 482 TYR cc_start: 0.8199 (m-10) cc_final: 0.7772 (m-10) REVERT: M 3 GLN cc_start: 0.8034 (mp10) cc_final: 0.7780 (mp10) REVERT: M 4 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8641 (mt) REVERT: M 421 MET cc_start: 0.8723 (mmm) cc_final: 0.8213 (mmm) REVERT: M 482 TYR cc_start: 0.8463 (m-80) cc_final: 0.8043 (m-80) outliers start: 46 outliers final: 36 residues processed: 345 average time/residue: 0.2792 time to fit residues: 148.1956 Evaluate side-chains 353 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 312 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 504 GLN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 464 ASN Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17291 Z= 0.239 Angle : 0.627 11.737 23577 Z= 0.308 Chirality : 0.045 0.251 2691 Planarity : 0.003 0.051 2900 Dihedral : 6.991 58.995 2920 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.03 % Allowed : 17.35 % Favored : 79.62 % 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: 1.19 (0.19), residues: 2024 helix: 1.66 (0.21), residues: 591 sheet: 0.89 (0.22), residues: 579 loop : 0.21 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 237 HIS 0.003 0.001 HIS E 240 PHE 0.021 0.001 PHE A 289 TYR 0.023 0.001 TYR B 299 ARG 0.007 0.000 ARG E 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 314 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6566 (mtp) cc_final: 0.6075 (mpp) REVERT: A 227 MET cc_start: 0.8285 (ttt) cc_final: 0.7924 (ttp) REVERT: A 429 ILE cc_start: 0.9008 (tp) cc_final: 0.8698 (mm) REVERT: A 445 TYR cc_start: 0.8106 (t80) cc_final: 0.7820 (t80) REVERT: B 55 MET cc_start: 0.8795 (mmt) cc_final: 0.8551 (mmt) REVERT: B 286 MET cc_start: 0.7865 (ttt) cc_final: 0.7417 (tmm) REVERT: C 18 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8812 (pttm) REVERT: C 52 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7514 (mm-30) REVERT: C 138 MET cc_start: 0.8734 (mtt) cc_final: 0.8385 (mtt) REVERT: C 298 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8399 (tm-30) REVERT: D 180 ARG cc_start: 0.7417 (mmp80) cc_final: 0.7040 (mmp80) REVERT: D 227 MET cc_start: 0.8596 (mmt) cc_final: 0.8273 (tpp) REVERT: D 243 ASN cc_start: 0.7555 (t0) cc_final: 0.7025 (t0) REVERT: E 83 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7904 (mmm) REVERT: E 128 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8596 (p0) REVERT: E 170 LYS cc_start: 0.8321 (mttt) cc_final: 0.7796 (mmmt) REVERT: E 177 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: E 179 MET cc_start: 0.7675 (mmm) cc_final: 0.7190 (mmm) REVERT: E 222 THR cc_start: 0.8718 (m) cc_final: 0.8472 (p) REVERT: E 253 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8000 (tp40) REVERT: E 290 MET cc_start: 0.8573 (mmm) cc_final: 0.8289 (tpt) REVERT: K 469 GLU cc_start: 0.7474 (mp0) cc_final: 0.6931 (mp0) REVERT: K 481 TYR cc_start: 0.7753 (m-80) cc_final: 0.7527 (m-10) REVERT: K 482 TYR cc_start: 0.8225 (m-10) cc_final: 0.7758 (m-10) REVERT: M 3 GLN cc_start: 0.8081 (mp10) cc_final: 0.7793 (mp10) REVERT: M 4 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8649 (mt) REVERT: M 421 MET cc_start: 0.8734 (mmm) cc_final: 0.8398 (mmm) REVERT: M 482 TYR cc_start: 0.8488 (m-80) cc_final: 0.8049 (m-80) outliers start: 49 outliers final: 38 residues processed: 339 average time/residue: 0.2684 time to fit residues: 139.9304 Evaluate side-chains 358 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 314 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 464 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 115 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 195 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 0.1980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN K 507 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17291 Z= 0.293 Angle : 0.646 12.457 23577 Z= 0.319 Chirality : 0.046 0.256 2691 Planarity : 0.003 0.040 2900 Dihedral : 6.987 58.837 2920 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.92 % Allowed : 17.41 % Favored : 79.67 % 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: 1.30 (0.19), residues: 2024 helix: 1.61 (0.21), residues: 613 sheet: 0.99 (0.22), residues: 568 loop : 0.34 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 237 HIS 0.004 0.001 HIS C 267 PHE 0.061 0.002 PHE K 455 TYR 0.034 0.002 TYR A 66 ARG 0.005 0.000 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 310 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6587 (mtp) cc_final: 0.6092 (mpp) REVERT: A 17 ASP cc_start: 0.9090 (t70) cc_final: 0.8663 (t0) REVERT: A 227 MET cc_start: 0.8313 (ttt) cc_final: 0.8012 (ttp) REVERT: A 429 ILE cc_start: 0.9018 (tp) cc_final: 0.8704 (mm) REVERT: A 445 TYR cc_start: 0.8113 (t80) cc_final: 0.7837 (t80) REVERT: B 55 MET cc_start: 0.8810 (mmt) cc_final: 0.8555 (mmt) REVERT: B 286 MET cc_start: 0.7879 (ttt) cc_final: 0.7384 (ttp) REVERT: C 18 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8806 (pttm) REVERT: C 52 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7523 (mm-30) REVERT: C 138 MET cc_start: 0.8723 (mtt) cc_final: 0.8364 (mtt) REVERT: C 298 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8416 (tm-30) REVERT: D 180 ARG cc_start: 0.7476 (mmp80) cc_final: 0.7113 (mmp80) REVERT: D 227 MET cc_start: 0.8615 (mmt) cc_final: 0.8282 (tpp) REVERT: D 243 ASN cc_start: 0.7567 (t0) cc_final: 0.7036 (t0) REVERT: E 83 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7884 (mmm) REVERT: E 128 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8590 (p0) REVERT: E 170 LYS cc_start: 0.8359 (mttt) cc_final: 0.7838 (mmmt) REVERT: E 177 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: E 179 MET cc_start: 0.7729 (mmm) cc_final: 0.7327 (mmm) REVERT: E 222 THR cc_start: 0.8726 (m) cc_final: 0.8445 (p) REVERT: E 290 MET cc_start: 0.8564 (mmm) cc_final: 0.8317 (tpt) REVERT: E 333 PHE cc_start: 0.8571 (t80) cc_final: 0.7912 (t80) REVERT: K 469 GLU cc_start: 0.7864 (mp0) cc_final: 0.7205 (mp0) REVERT: K 481 TYR cc_start: 0.7870 (m-80) cc_final: 0.7667 (m-10) REVERT: K 482 TYR cc_start: 0.8301 (m-10) cc_final: 0.7814 (m-10) REVERT: M 3 GLN cc_start: 0.8057 (mp10) cc_final: 0.7770 (mp10) REVERT: M 4 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8659 (mt) REVERT: M 474 LYS cc_start: 0.8893 (mttt) cc_final: 0.8412 (mttt) REVERT: M 482 TYR cc_start: 0.8522 (m-80) cc_final: 0.8082 (m-80) outliers start: 47 outliers final: 39 residues processed: 337 average time/residue: 0.2692 time to fit residues: 139.9816 Evaluate side-chains 348 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 304 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 464 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: 0.9980 chunk 165 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.064331 restraints weight = 246817.803| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 7.29 r_work: 0.2716 rms_B_bonded: 6.35 restraints_weight: 2.0000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17291 Z= 0.167 Angle : 0.634 14.956 23577 Z= 0.306 Chirality : 0.045 0.243 2691 Planarity : 0.003 0.032 2900 Dihedral : 6.579 54.339 2920 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.19 % Allowed : 18.30 % Favored : 79.51 % 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: 1.27 (0.19), residues: 2024 helix: 1.61 (0.21), residues: 613 sheet: 0.89 (0.22), residues: 577 loop : 0.36 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 237 HIS 0.003 0.000 HIS E 240 PHE 0.044 0.001 PHE K 455 TYR 0.028 0.001 TYR D 446 ARG 0.010 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.39 seconds wall clock time: 79 minutes 31.28 seconds (4771.28 seconds total)