Starting phenix.real_space_refine on Sun Mar 17 05:11:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn8_14070/03_2024/7qn8_14070_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn8_14070/03_2024/7qn8_14070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn8_14070/03_2024/7qn8_14070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn8_14070/03_2024/7qn8_14070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn8_14070/03_2024/7qn8_14070_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn8_14070/03_2024/7qn8_14070_updated.pdb" } resolution = 3.1 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= 0.004 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 10897 2.51 5 N 2698 2.21 5 O 3071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16755 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2749 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2683 Chain: "B" Number of atoms: 2753 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: 2678 Chain: "C" Number of atoms: 2754 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: 2677 Chain: "D" Number of atoms: 2716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2721 Chain: "E" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2569 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'HSM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N ALEU A 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 125 " occ=0.50 residue: pdb=" N ASER A 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 209 " occ=0.50 residue: pdb=" N ALEU A 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 214 " occ=0.50 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N ASER B 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 209 " occ=0.50 residue: pdb=" N ALEU B 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 214 " occ=0.50 residue: pdb=" N ASER B 229 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 229 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N ATYR C 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 66 " occ=0.50 residue: pdb=" N ALEU C 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 125 " occ=0.50 residue: pdb=" N ASER C 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 209 " occ=0.50 residue: pdb=" N ASER D 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 209 " occ=0.50 Time building chain proxies: 13.94, per 1000 atoms: 0.83 Number of scatterers: 16755 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 3071 8.00 N 2698 7.00 C 10897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 483 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG E 501 " - " ASN E 103 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 149 " " NAG H 1 " - " ASN C 149 " " NAG I 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 80 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 5.1 seconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 28 sheets defined 31.6% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.531A 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: 3.545A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.513A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.681A 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 Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.531A 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: 3.545A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.513A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.681A 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 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.531A 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: 3.545A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.513A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.681A 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 Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.530A 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: 3.544A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.513A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.680A 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 Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 45 through 48 No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 118 removed outlier: 4.089A 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 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 249 through 270 removed outlier: 3.855A pdb=" N SER E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) Proline residue: E 257 - end of helix removed outlier: 3.807A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 300 Processing helix chain 'E' and resid 309 through 335 removed outlier: 3.542A pdb=" N LEU E 325 " --> pdb=" O VAL E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 450 removed outlier: 3.711A pdb=" N ALA E 433 " --> pdb=" O ILE E 429 " (cutoff:3.500A) 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: 6.276A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.445A 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: 4.052A 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: 3.915A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.843A 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: 6.689A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.979A 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: 6.277A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.446A 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: 4.051A 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: 3.914A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.843A 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: 6.688A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.981A 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: 6.276A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.446A 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: 4.052A 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: 3.915A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.844A 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: 6.689A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.981A 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: 6.277A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.446A 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: 4.051A 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: 3.914A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.844A 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: 6.689A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.980A 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: 6.165A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 144 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 124 through 126 removed outlier: 3.982A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 129 through 134 removed outlier: 6.748A pdb=" N THR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA E 132 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR E 159 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 2 through 7 Processing sheet with id= U, first strand: chain 'K' and resid 506 through 508 removed outlier: 3.870A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG K 425 " --> pdb=" O PHE K 434 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N PHE K 434 " --> pdb=" O ARG K 425 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 484 through 486 removed outlier: 3.829A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 2 through 7 Processing sheet with id= X, first strand: chain 'L' and resid 506 through 508 removed outlier: 3.870A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 484 through 486 removed outlier: 3.830A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 2 through 7 Processing sheet with id= AA, first strand: chain 'M' and resid 506 through 508 removed outlier: 3.870A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 484 through 486 removed outlier: 3.830A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2171 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: 5.30 Time building geometry restraints manager: 7.63 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: 5099 1.34 - 1.46: 4312 1.46 - 1.58: 7663 1.58 - 1.69: 0 1.69 - 1.81: 153 Bond restraints: 17227 Sorted by residual: 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 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 2.17e+00 bond pdb=" C1 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.14e+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 2.13e+00 bond pdb=" C1 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.399 1.427 -0.028 2.00e-02 2.50e+03 2.03e+00 ... (remaining 17222 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.05: 494 107.05 - 113.78: 9663 113.78 - 120.52: 6479 120.52 - 127.25: 6656 127.25 - 133.99: 192 Bond angle restraints: 23484 Sorted by residual: angle pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " pdb=" C5 BMA F 3 " ideal model delta sigma weight residual 118.82 113.39 5.43 3.00e+00 1.11e-01 3.28e+00 angle pdb=" C1 BMA G 3 " pdb=" O5 BMA G 3 " pdb=" C5 BMA G 3 " ideal model delta sigma weight residual 118.82 113.49 5.33 3.00e+00 1.11e-01 3.16e+00 angle pdb=" C1 BMA H 3 " pdb=" O5 BMA H 3 " pdb=" C5 BMA H 3 " ideal model delta sigma weight residual 118.82 113.58 5.24 3.00e+00 1.11e-01 3.05e+00 angle pdb=" C1 BMA I 3 " pdb=" O5 BMA I 3 " pdb=" C5 BMA I 3 " ideal model delta sigma weight residual 118.82 113.72 5.10 3.00e+00 1.11e-01 2.89e+00 angle pdb=" CA TYR D 66 " pdb=" CB TYR D 66 " pdb=" CG TYR D 66 " ideal model delta sigma weight residual 113.90 116.87 -2.97 1.80e+00 3.09e-01 2.72e+00 ... (remaining 23479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.19: 10227 21.19 - 42.38: 149 42.38 - 63.57: 19 63.57 - 84.76: 34 84.76 - 105.95: 17 Dihedral angle restraints: 10446 sinusoidal: 4457 harmonic: 5989 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 -177.24 105.95 1 3.00e+01 1.11e-03 1.36e+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 -176.97 105.68 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.46 105.17 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 10443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2299 0.054 - 0.109: 342 0.109 - 0.163: 36 0.163 - 0.218: 7 0.218 - 0.272: 5 Chirality restraints: 2689 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 -2.31 -0.09 2.00e-02 2.50e+03 1.89e+01 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.79e+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 2.32 0.08 2.00e-02 2.50e+03 1.64e+01 ... (remaining 2686 not shown) Planarity restraints: 2899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " -0.022 2.00e-02 2.50e+03 1.83e-02 4.19e+00 pdb=" C7 NAG E 501 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " -0.017 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " 0.029 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 65 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.21e+00 pdb=" C GLN C 65 " 0.019 2.00e-02 2.50e+03 pdb=" O GLN C 65 " -0.007 2.00e-02 2.50e+03 pdb=" N BTYR C 66 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 65 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C GLN D 65 " -0.019 2.00e-02 2.50e+03 pdb=" O GLN D 65 " 0.007 2.00e-02 2.50e+03 pdb=" N TYR D 66 " 0.006 2.00e-02 2.50e+03 ... (remaining 2896 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3119 2.78 - 3.31: 15563 3.31 - 3.84: 28763 3.84 - 4.37: 35411 4.37 - 4.90: 60203 Nonbonded interactions: 143059 Sorted by model distance: nonbonded pdb=" ND2AASN A 41 " pdb=" O ARG A 169 " model vdw 2.247 2.520 nonbonded pdb=" OH TYR E 171 " pdb=" OH TYR E 250 " model vdw 2.256 2.440 nonbonded pdb=" ND2AASN C 41 " pdb=" O ARG C 169 " model vdw 2.274 2.520 nonbonded pdb=" ND2AASN B 41 " pdb=" O ARG B 169 " model vdw 2.275 2.520 nonbonded pdb=" OE2 GLU L 6 " pdb=" N GLY L 505 " model vdw 2.308 2.520 ... (remaining 143054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 447)) selection = (chain 'B' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 447)) selection = (chain 'C' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 447)) selection = (chain 'D' and (resid 7 through 40 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 65 or resid 67 through 103 or resid 105 through 111 or resi \ d 113 through 124 or resid 126 through 208 or resid 210 through 213 or resid 215 \ through 228 or resid 230 through 240 or resid 243 through 252 or resid 254 thro \ ugh 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 5.970 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 55.820 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 0.030 17227 Z= 0.164 Angle : 0.456 5.435 23484 Z= 0.210 Chirality : 0.042 0.272 2689 Planarity : 0.003 0.027 2890 Dihedral : 10.683 105.946 6616 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.34 % Allowed : 2.03 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.21 (0.19), residues: 2022 helix: 2.51 (0.21), residues: 551 sheet: 1.35 (0.22), residues: 630 loop : 0.99 (0.23), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 443 HIS 0.002 0.001 HIS D 267 PHE 0.008 0.001 PHE E 90 TYR 0.015 0.001 TYR D 66 ARG 0.002 0.000 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 415 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8470 (tttp) cc_final: 0.8113 (tttp) REVERT: A 224 GLN cc_start: 0.8499 (tp40) cc_final: 0.8211 (tp40) REVERT: A 283 MET cc_start: 0.8438 (mmm) cc_final: 0.8226 (mmt) REVERT: A 298 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 157 TYR cc_start: 0.8862 (t80) cc_final: 0.8572 (t80) REVERT: B 215 LYS cc_start: 0.8874 (tttt) cc_final: 0.8648 (ttmm) REVERT: B 243 ASN cc_start: 0.7795 (t0) cc_final: 0.7589 (t0) REVERT: B 306 PHE cc_start: 0.8334 (t80) cc_final: 0.8020 (t80) REVERT: C 224 GLN cc_start: 0.8580 (tp40) cc_final: 0.8268 (tp40) REVERT: C 243 ASN cc_start: 0.7572 (t0) cc_final: 0.6923 (t0) REVERT: D 52 GLU cc_start: 0.8257 (mp0) cc_final: 0.7992 (mp0) REVERT: E 80 GLU cc_start: 0.8251 (pm20) cc_final: 0.8020 (mp0) REVERT: E 83 MET cc_start: 0.9073 (mmm) cc_final: 0.8690 (mmt) REVERT: E 118 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8582 (mppt) REVERT: E 170 LYS cc_start: 0.8615 (mttt) cc_final: 0.8393 (mtpp) REVERT: E 173 MET cc_start: 0.8398 (mpp) cc_final: 0.8166 (mpp) REVERT: E 210 GLN cc_start: 0.8517 (mt0) cc_final: 0.8192 (mt0) REVERT: E 253 GLN cc_start: 0.7181 (tt0) cc_final: 0.6780 (tm-30) REVERT: K 414 HIS cc_start: 0.7084 (m90) cc_final: 0.6749 (m170) REVERT: K 470 MET cc_start: 0.8109 (mtm) cc_final: 0.6996 (mtm) REVERT: K 481 TYR cc_start: 0.5826 (m-80) cc_final: 0.3814 (m-10) REVERT: L 455 PHE cc_start: 0.8373 (m-10) cc_final: 0.8072 (m-10) REVERT: L 481 TYR cc_start: 0.7708 (m-80) cc_final: 0.7158 (m-80) REVERT: M 455 PHE cc_start: 0.8272 (m-10) cc_final: 0.7877 (m-10) REVERT: M 474 LYS cc_start: 0.9025 (mttt) cc_final: 0.8304 (mttp) outliers start: 6 outliers final: 3 residues processed: 421 average time/residue: 0.3165 time to fit residues: 191.4512 Evaluate side-chains 242 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 228 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.0980 chunk 148 optimal weight: 0.0010 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 267 HIS B 267 HIS E 443 ASN K 461 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17227 Z= 0.178 Angle : 0.602 13.171 23484 Z= 0.306 Chirality : 0.044 0.209 2689 Planarity : 0.004 0.045 2890 Dihedral : 8.912 78.548 2899 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.41 % Allowed : 9.06 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.13 (0.19), residues: 2022 helix: 2.81 (0.22), residues: 543 sheet: 1.04 (0.21), residues: 651 loop : 0.91 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 315 HIS 0.015 0.001 HIS B 267 PHE 0.022 0.002 PHE D 433 TYR 0.020 0.001 TYR E 318 ARG 0.007 0.000 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 249 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8385 (tp40) cc_final: 0.8158 (tp40) REVERT: A 283 MET cc_start: 0.8384 (mmm) cc_final: 0.8138 (mmt) REVERT: B 243 ASN cc_start: 0.7870 (t0) cc_final: 0.7651 (t0) REVERT: B 306 PHE cc_start: 0.8322 (t80) cc_final: 0.8014 (t80) REVERT: C 224 GLN cc_start: 0.8480 (tp40) cc_final: 0.8194 (tp40) REVERT: C 243 ASN cc_start: 0.7574 (t0) cc_final: 0.7104 (t0) REVERT: E 83 MET cc_start: 0.9104 (mmm) cc_final: 0.8742 (mmt) REVERT: E 170 LYS cc_start: 0.8692 (mttt) cc_final: 0.8473 (mtpp) REVERT: E 264 MET cc_start: 0.8997 (ttm) cc_final: 0.8741 (ttm) REVERT: L 460 ASP cc_start: 0.8235 (t0) cc_final: 0.7828 (t0) REVERT: L 474 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8610 (mmmt) REVERT: L 482 TYR cc_start: 0.8509 (m-80) cc_final: 0.8186 (m-80) REVERT: M 426 GLN cc_start: 0.7667 (pt0) cc_final: 0.7425 (pt0) REVERT: M 466 VAL cc_start: 0.9154 (t) cc_final: 0.8899 (m) REVERT: M 482 TYR cc_start: 0.8277 (m-80) cc_final: 0.7118 (m-80) outliers start: 25 outliers final: 12 residues processed: 266 average time/residue: 0.2922 time to fit residues: 116.6823 Evaluate side-chains 234 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 222 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 456 THR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17227 Z= 0.280 Angle : 0.599 15.438 23484 Z= 0.304 Chirality : 0.045 0.224 2689 Planarity : 0.003 0.034 2890 Dihedral : 8.387 71.484 2899 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.14 % Allowed : 8.89 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.97 (0.19), residues: 2022 helix: 2.66 (0.22), residues: 549 sheet: 0.99 (0.21), residues: 651 loop : 0.77 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 315 HIS 0.004 0.001 HIS A 119 PHE 0.019 0.002 PHE D 433 TYR 0.025 0.002 TYR L 481 ARG 0.006 0.001 ARG M 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 238 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8084 (mmm) cc_final: 0.7671 (tpt) REVERT: A 224 GLN cc_start: 0.8358 (tp40) cc_final: 0.8105 (tp40) REVERT: B 224 GLN cc_start: 0.8439 (tp40) cc_final: 0.8159 (tp40) REVERT: B 243 ASN cc_start: 0.7889 (t0) cc_final: 0.7653 (t0) REVERT: B 306 PHE cc_start: 0.8348 (t80) cc_final: 0.8055 (t80) REVERT: C 224 GLN cc_start: 0.8513 (tp40) cc_final: 0.8258 (tp40) REVERT: C 243 ASN cc_start: 0.7705 (t0) cc_final: 0.7230 (t0) REVERT: D 227 MET cc_start: 0.8620 (mmm) cc_final: 0.7966 (mmm) REVERT: E 83 MET cc_start: 0.9092 (mmm) cc_final: 0.8768 (mmt) REVERT: E 104 HIS cc_start: 0.5805 (OUTLIER) cc_final: 0.5388 (t-90) REVERT: E 170 LYS cc_start: 0.8736 (mttt) cc_final: 0.8487 (mtpp) REVERT: E 264 MET cc_start: 0.9039 (ttm) cc_final: 0.8815 (ttm) REVERT: K 463 LYS cc_start: 0.7580 (pttt) cc_final: 0.7367 (pttp) REVERT: L 433 GLU cc_start: 0.7835 (tt0) cc_final: 0.7619 (pt0) REVERT: L 460 ASP cc_start: 0.8229 (t0) cc_final: 0.7908 (t0) REVERT: L 472 ASN cc_start: 0.8384 (t0) cc_final: 0.8039 (t0) REVERT: L 474 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8690 (mmmm) REVERT: L 482 TYR cc_start: 0.8659 (m-80) cc_final: 0.8250 (m-80) REVERT: M 469 GLU cc_start: 0.8331 (mp0) cc_final: 0.7889 (mp0) outliers start: 37 outliers final: 22 residues processed: 256 average time/residue: 0.2721 time to fit residues: 106.5562 Evaluate side-chains 240 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 228 PHE 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 478 THR Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17227 Z= 0.335 Angle : 0.602 10.305 23484 Z= 0.306 Chirality : 0.045 0.239 2689 Planarity : 0.003 0.029 2890 Dihedral : 8.149 67.471 2899 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.48 % Allowed : 10.24 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.84 (0.19), residues: 2022 helix: 2.68 (0.22), residues: 549 sheet: 0.92 (0.21), residues: 647 loop : 0.57 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 315 HIS 0.004 0.001 HIS C 107 PHE 0.023 0.002 PHE C 433 TYR 0.026 0.002 TYR B 299 ARG 0.004 0.001 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8431 (p0) cc_final: 0.8157 (p0) REVERT: A 224 GLN cc_start: 0.8458 (tp40) cc_final: 0.8146 (tp40) REVERT: B 243 ASN cc_start: 0.7903 (t0) cc_final: 0.7671 (t0) REVERT: B 306 PHE cc_start: 0.8294 (t80) cc_final: 0.6766 (t80) REVERT: C 224 GLN cc_start: 0.8595 (tp40) cc_final: 0.8341 (tp40) REVERT: C 243 ASN cc_start: 0.7817 (t0) cc_final: 0.7358 (t0) REVERT: D 40 MET cc_start: 0.8286 (mtt) cc_final: 0.8006 (mtt) REVERT: D 227 MET cc_start: 0.8538 (mmm) cc_final: 0.7964 (mmm) REVERT: E 83 MET cc_start: 0.9084 (mmm) cc_final: 0.8768 (mmt) REVERT: E 104 HIS cc_start: 0.5779 (OUTLIER) cc_final: 0.5330 (t-90) REVERT: E 166 MET cc_start: 0.8715 (mtp) cc_final: 0.8486 (mtp) REVERT: E 170 LYS cc_start: 0.8806 (mttt) cc_final: 0.8557 (mtpp) REVERT: E 256 MET cc_start: 0.8233 (tpp) cc_final: 0.8032 (tpp) REVERT: K 472 ASN cc_start: 0.7630 (t0) cc_final: 0.6289 (t0) REVERT: L 433 GLU cc_start: 0.7802 (tt0) cc_final: 0.7592 (pt0) REVERT: L 472 ASN cc_start: 0.8328 (t0) cc_final: 0.8126 (t0) REVERT: L 474 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8696 (mmmm) REVERT: L 482 TYR cc_start: 0.8733 (m-80) cc_final: 0.8228 (m-80) REVERT: M 460 ASP cc_start: 0.7962 (t70) cc_final: 0.7293 (p0) REVERT: M 469 GLU cc_start: 0.8316 (mp0) cc_final: 0.7831 (mp0) outliers start: 43 outliers final: 28 residues processed: 251 average time/residue: 0.2932 time to fit residues: 109.4682 Evaluate side-chains 240 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain K residue 1 GLN 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 5 VAL Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain M residue 430 LYS Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 2 optimal weight: 0.0770 chunk 141 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A M 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17227 Z= 0.245 Angle : 0.566 12.489 23484 Z= 0.284 Chirality : 0.044 0.238 2689 Planarity : 0.003 0.043 2890 Dihedral : 7.775 63.893 2898 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.19 % Allowed : 11.20 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.81 (0.19), residues: 2022 helix: 2.69 (0.22), residues: 546 sheet: 0.95 (0.21), residues: 647 loop : 0.49 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 315 HIS 0.002 0.001 HIS C 107 PHE 0.017 0.002 PHE C 433 TYR 0.024 0.002 TYR B 244 ARG 0.009 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 223 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8393 (tpp) cc_final: 0.7532 (mmm) REVERT: A 95 ASP cc_start: 0.8462 (p0) cc_final: 0.8242 (p0) REVERT: A 224 GLN cc_start: 0.8456 (tp40) cc_final: 0.8176 (tp40) REVERT: B 49 MET cc_start: 0.7836 (ptm) cc_final: 0.7510 (ppp) REVERT: B 243 ASN cc_start: 0.7806 (t0) cc_final: 0.7581 (t0) REVERT: C 224 GLN cc_start: 0.8560 (tp40) cc_final: 0.8328 (tp40) REVERT: C 243 ASN cc_start: 0.7822 (t0) cc_final: 0.7367 (t0) REVERT: D 40 MET cc_start: 0.8259 (mtt) cc_final: 0.7923 (mtt) REVERT: D 227 MET cc_start: 0.8555 (mmm) cc_final: 0.8002 (mmm) REVERT: D 437 LEU cc_start: 0.8548 (tt) cc_final: 0.8150 (mp) REVERT: E 83 MET cc_start: 0.9081 (mmm) cc_final: 0.8826 (mmt) REVERT: E 104 HIS cc_start: 0.5738 (OUTLIER) cc_final: 0.5297 (t-90) REVERT: E 166 MET cc_start: 0.8741 (mtp) cc_final: 0.8451 (mtp) REVERT: E 170 LYS cc_start: 0.8797 (mttt) cc_final: 0.8551 (mtpp) REVERT: K 459 ARG cc_start: 0.7982 (pmt-80) cc_final: 0.7182 (ppt170) REVERT: K 460 ASP cc_start: 0.7766 (t0) cc_final: 0.7509 (t0) REVERT: K 468 LEU cc_start: 0.8588 (tp) cc_final: 0.8309 (tp) REVERT: K 470 MET cc_start: 0.8169 (mtm) cc_final: 0.7569 (mpp) REVERT: K 472 ASN cc_start: 0.7391 (t0) cc_final: 0.6839 (t0) REVERT: L 474 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8613 (mmmm) REVERT: L 482 TYR cc_start: 0.8753 (m-80) cc_final: 0.8171 (m-80) REVERT: M 460 ASP cc_start: 0.8015 (t70) cc_final: 0.7701 (p0) REVERT: M 469 GLU cc_start: 0.8318 (mp0) cc_final: 0.7748 (mp0) REVERT: M 481 TYR cc_start: 0.8209 (m-80) cc_final: 0.7787 (m-10) outliers start: 38 outliers final: 33 residues processed: 243 average time/residue: 0.2815 time to fit residues: 104.1505 Evaluate side-chains 252 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 218 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain K residue 1 GLN Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 456 THR Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain K residue 508 VAL Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 VAL Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 99 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17227 Z= 0.165 Angle : 0.544 13.134 23484 Z= 0.269 Chirality : 0.043 0.241 2689 Planarity : 0.003 0.031 2890 Dihedral : 7.106 58.106 2898 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.80 % Allowed : 11.87 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.88 (0.19), residues: 2022 helix: 2.73 (0.22), residues: 546 sheet: 1.00 (0.21), residues: 649 loop : 0.54 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 315 HIS 0.002 0.001 HIS E 240 PHE 0.017 0.001 PHE C 433 TYR 0.022 0.001 TYR B 299 ARG 0.006 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 225 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8454 (p0) cc_final: 0.8236 (p0) REVERT: A 224 GLN cc_start: 0.8407 (tp40) cc_final: 0.8168 (tp40) REVERT: A 286 MET cc_start: 0.7982 (mmp) cc_final: 0.7735 (ppp) REVERT: B 49 MET cc_start: 0.7796 (ptm) cc_final: 0.7558 (ppp) REVERT: B 243 ASN cc_start: 0.7865 (t0) cc_final: 0.7640 (t0) REVERT: C 224 GLN cc_start: 0.8542 (tp40) cc_final: 0.8299 (tp40) REVERT: C 243 ASN cc_start: 0.7800 (t0) cc_final: 0.6962 (t0) REVERT: D 40 MET cc_start: 0.8253 (mtt) cc_final: 0.7951 (mtt) REVERT: D 227 MET cc_start: 0.8550 (mmm) cc_final: 0.8011 (mmm) REVERT: D 437 LEU cc_start: 0.8589 (tt) cc_final: 0.8201 (mp) REVERT: E 83 MET cc_start: 0.9077 (mmm) cc_final: 0.8823 (mmt) REVERT: E 104 HIS cc_start: 0.5878 (OUTLIER) cc_final: 0.5444 (t-90) REVERT: E 166 MET cc_start: 0.8705 (mtp) cc_final: 0.8390 (mtp) REVERT: E 170 LYS cc_start: 0.8789 (mttt) cc_final: 0.8548 (mtpp) REVERT: K 3 GLN cc_start: 0.8406 (mp10) cc_final: 0.8120 (mp10) REVERT: K 459 ARG cc_start: 0.8114 (pmt-80) cc_final: 0.7392 (ppt170) REVERT: K 460 ASP cc_start: 0.7760 (t0) cc_final: 0.7494 (t0) REVERT: K 472 ASN cc_start: 0.7265 (t0) cc_final: 0.6056 (t0) REVERT: K 474 LYS cc_start: 0.8360 (mmtp) cc_final: 0.7492 (mmtp) REVERT: L 474 LYS cc_start: 0.8866 (mmmm) cc_final: 0.8627 (mmmm) REVERT: L 482 TYR cc_start: 0.8763 (m-80) cc_final: 0.8228 (m-80) REVERT: M 460 ASP cc_start: 0.8031 (t70) cc_final: 0.7760 (p0) outliers start: 31 outliers final: 23 residues processed: 243 average time/residue: 0.2706 time to fit residues: 99.8332 Evaluate side-chains 241 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 217 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 228 PHE 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 478 THR Chi-restraints excluded: chain L residue 480 VAL Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 0.0270 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17227 Z= 0.246 Angle : 0.563 12.899 23484 Z= 0.281 Chirality : 0.044 0.245 2689 Planarity : 0.003 0.030 2890 Dihedral : 7.064 57.284 2898 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.03 % Allowed : 11.59 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.84 (0.19), residues: 2022 helix: 2.71 (0.22), residues: 541 sheet: 1.01 (0.21), residues: 649 loop : 0.49 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 315 HIS 0.008 0.001 HIS E 240 PHE 0.018 0.001 PHE B 306 TYR 0.024 0.002 TYR B 299 ARG 0.005 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 221 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8461 (p0) cc_final: 0.8235 (p0) REVERT: A 224 GLN cc_start: 0.8449 (tp40) cc_final: 0.8223 (tp40) REVERT: A 286 MET cc_start: 0.8039 (mmp) cc_final: 0.7737 (ppp) REVERT: B 243 ASN cc_start: 0.7869 (t0) cc_final: 0.7655 (t0) REVERT: C 224 GLN cc_start: 0.8556 (tp40) cc_final: 0.8304 (tp40) REVERT: C 243 ASN cc_start: 0.7842 (t0) cc_final: 0.7042 (t0) REVERT: D 40 MET cc_start: 0.8264 (mtt) cc_final: 0.7937 (mtt) REVERT: D 227 MET cc_start: 0.8563 (mmm) cc_final: 0.8035 (mmm) REVERT: E 83 MET cc_start: 0.9095 (mmm) cc_final: 0.8880 (mmt) REVERT: E 104 HIS cc_start: 0.5918 (OUTLIER) cc_final: 0.5457 (t-90) REVERT: E 166 MET cc_start: 0.8701 (mtp) cc_final: 0.8487 (mtp) REVERT: E 170 LYS cc_start: 0.8794 (mttt) cc_final: 0.8549 (mtpp) REVERT: K 3 GLN cc_start: 0.8425 (mp10) cc_final: 0.8141 (mp10) REVERT: K 459 ARG cc_start: 0.8164 (pmt-80) cc_final: 0.7672 (ppt170) REVERT: K 472 ASN cc_start: 0.7415 (t0) cc_final: 0.6531 (t0) REVERT: K 474 LYS cc_start: 0.8447 (mmtp) cc_final: 0.7758 (mmtp) REVERT: L 482 TYR cc_start: 0.8821 (m-80) cc_final: 0.8301 (m-80) REVERT: M 460 ASP cc_start: 0.8058 (t70) cc_final: 0.7813 (p0) REVERT: M 480 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8611 (p) outliers start: 34 outliers final: 29 residues processed: 239 average time/residue: 0.2935 time to fit residues: 106.4269 Evaluate side-chains 246 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain K residue 1 GLN Chi-restraints excluded: chain K residue 4 LEU 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 478 THR Chi-restraints excluded: chain L residue 480 VAL Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 407 LEU Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 56 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17227 Z= 0.216 Angle : 0.563 12.932 23484 Z= 0.280 Chirality : 0.044 0.245 2689 Planarity : 0.003 0.038 2890 Dihedral : 6.856 55.341 2898 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.08 % Allowed : 11.93 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.86 (0.19), residues: 2022 helix: 2.74 (0.22), residues: 541 sheet: 1.03 (0.21), residues: 649 loop : 0.47 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 315 HIS 0.002 0.001 HIS C 107 PHE 0.018 0.001 PHE B 306 TYR 0.032 0.001 TYR D 220 ARG 0.007 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8466 (p0) cc_final: 0.8239 (p0) REVERT: A 224 GLN cc_start: 0.8446 (tp40) cc_final: 0.8217 (tp40) REVERT: A 286 MET cc_start: 0.8040 (mmp) cc_final: 0.7775 (ppp) REVERT: B 243 ASN cc_start: 0.7886 (t0) cc_final: 0.7678 (t0) REVERT: C 224 GLN cc_start: 0.8553 (tp40) cc_final: 0.8305 (tp40) REVERT: C 243 ASN cc_start: 0.7859 (t0) cc_final: 0.7067 (t0) REVERT: D 40 MET cc_start: 0.8253 (mtt) cc_final: 0.7932 (mtt) REVERT: D 227 MET cc_start: 0.8549 (mmm) cc_final: 0.8013 (mmm) REVERT: D 437 LEU cc_start: 0.8564 (tt) cc_final: 0.8168 (mp) REVERT: E 83 MET cc_start: 0.9098 (mmm) cc_final: 0.8849 (mmt) REVERT: E 104 HIS cc_start: 0.5893 (OUTLIER) cc_final: 0.5452 (t70) REVERT: E 166 MET cc_start: 0.8683 (mtp) cc_final: 0.8440 (mtp) REVERT: E 170 LYS cc_start: 0.8796 (mttt) cc_final: 0.8545 (mtpp) REVERT: E 260 LEU cc_start: 0.9036 (pp) cc_final: 0.8763 (mt) REVERT: K 3 GLN cc_start: 0.8424 (mp10) cc_final: 0.8142 (mp10) REVERT: K 459 ARG cc_start: 0.8112 (pmt-80) cc_final: 0.7790 (ppt170) REVERT: K 472 ASN cc_start: 0.7342 (t0) cc_final: 0.6806 (t0) REVERT: L 472 ASN cc_start: 0.8541 (t0) cc_final: 0.8211 (t0) REVERT: L 474 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8531 (mmmt) REVERT: L 482 TYR cc_start: 0.8811 (m-80) cc_final: 0.8294 (m-80) REVERT: M 460 ASP cc_start: 0.8068 (t70) cc_final: 0.7825 (p0) REVERT: M 469 GLU cc_start: 0.8151 (mp0) cc_final: 0.7706 (mp0) REVERT: M 480 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8602 (p) outliers start: 35 outliers final: 30 residues processed: 233 average time/residue: 0.2858 time to fit residues: 100.5280 Evaluate side-chains 245 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 213 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain K residue 1 GLN Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 461 ASN Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 VAL Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 407 LEU Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 105 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17227 Z= 0.134 Angle : 0.541 12.903 23484 Z= 0.266 Chirality : 0.043 0.243 2689 Planarity : 0.003 0.034 2890 Dihedral : 6.271 55.886 2898 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.63 % Allowed : 12.38 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2022 helix: 2.74 (0.22), residues: 541 sheet: 1.10 (0.21), residues: 649 loop : 0.54 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 315 HIS 0.002 0.000 HIS E 240 PHE 0.018 0.001 PHE B 306 TYR 0.024 0.001 TYR D 220 ARG 0.007 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8410 (p0) cc_final: 0.8198 (p0) REVERT: A 224 GLN cc_start: 0.8416 (tp40) cc_final: 0.8206 (tp40) REVERT: A 286 MET cc_start: 0.8004 (mmp) cc_final: 0.7738 (ppp) REVERT: B 49 MET cc_start: 0.7817 (ptm) cc_final: 0.7585 (ppp) REVERT: B 243 ASN cc_start: 0.7871 (t0) cc_final: 0.7657 (t0) REVERT: C 224 GLN cc_start: 0.8623 (tp40) cc_final: 0.8318 (tp40) REVERT: C 243 ASN cc_start: 0.7842 (t0) cc_final: 0.7067 (t0) REVERT: D 40 MET cc_start: 0.8261 (mtt) cc_final: 0.7964 (mtt) REVERT: D 227 MET cc_start: 0.8560 (mmm) cc_final: 0.8033 (mmm) REVERT: D 437 LEU cc_start: 0.8640 (tt) cc_final: 0.8248 (mp) REVERT: E 83 MET cc_start: 0.9074 (mmm) cc_final: 0.8849 (mmt) REVERT: E 104 HIS cc_start: 0.5802 (OUTLIER) cc_final: 0.5384 (t70) REVERT: E 166 MET cc_start: 0.8659 (mtp) cc_final: 0.8407 (mtp) REVERT: E 170 LYS cc_start: 0.8786 (mttt) cc_final: 0.8535 (mtpp) REVERT: K 3 GLN cc_start: 0.8415 (mp10) cc_final: 0.8141 (mp10) REVERT: K 459 ARG cc_start: 0.8110 (pmt-80) cc_final: 0.7785 (ppt170) REVERT: K 472 ASN cc_start: 0.7306 (t0) cc_final: 0.6454 (t0) REVERT: K 474 LYS cc_start: 0.8400 (mmtp) cc_final: 0.7657 (mmtp) REVERT: L 482 TYR cc_start: 0.8807 (m-80) cc_final: 0.8216 (m-80) REVERT: M 459 ARG cc_start: 0.8439 (pmt-80) cc_final: 0.7936 (pmt-80) REVERT: M 460 ASP cc_start: 0.8088 (t70) cc_final: 0.7852 (p0) REVERT: M 469 GLU cc_start: 0.8136 (mp0) cc_final: 0.7787 (mp0) REVERT: M 480 VAL cc_start: 0.8773 (t) cc_final: 0.8522 (p) outliers start: 27 outliers final: 23 residues processed: 241 average time/residue: 0.2814 time to fit residues: 101.8951 Evaluate side-chains 244 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 220 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain K residue 1 GLN Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 VAL Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 407 LEU 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: 1.9990 chunk 186 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 129 optimal weight: 0.0770 chunk 195 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 chunk 155 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B B 64 GLN C 41 ASN B C 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17227 Z= 0.140 Angle : 0.552 12.489 23484 Z= 0.268 Chirality : 0.043 0.244 2689 Planarity : 0.003 0.031 2890 Dihedral : 6.015 55.620 2898 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.69 % Allowed : 12.55 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.94 (0.19), residues: 2022 helix: 2.71 (0.22), residues: 541 sheet: 1.13 (0.21), residues: 633 loop : 0.56 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 315 HIS 0.002 0.000 HIS A 267 PHE 0.018 0.001 PHE B 306 TYR 0.021 0.001 TYR B 299 ARG 0.005 0.000 ARG D 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 228 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8221 (mmm) cc_final: 0.7558 (mmm) REVERT: A 95 ASP cc_start: 0.8379 (p0) cc_final: 0.8140 (p0) REVERT: A 286 MET cc_start: 0.7989 (mmp) cc_final: 0.7703 (ppp) REVERT: A 294 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8526 (tp) REVERT: B 49 MET cc_start: 0.7817 (ptm) cc_final: 0.7592 (ppp) REVERT: B 243 ASN cc_start: 0.7914 (t0) cc_final: 0.7683 (t0) REVERT: C 224 GLN cc_start: 0.8626 (tp40) cc_final: 0.7086 (tp40) REVERT: C 243 ASN cc_start: 0.7853 (t0) cc_final: 0.7080 (t0) REVERT: D 40 MET cc_start: 0.8258 (mtt) cc_final: 0.7962 (mtt) REVERT: D 227 MET cc_start: 0.8543 (mmm) cc_final: 0.8008 (mmm) REVERT: D 437 LEU cc_start: 0.8638 (tt) cc_final: 0.8245 (mp) REVERT: E 83 MET cc_start: 0.9070 (mmm) cc_final: 0.8825 (mmt) REVERT: E 104 HIS cc_start: 0.5773 (OUTLIER) cc_final: 0.5373 (t70) REVERT: E 166 MET cc_start: 0.8673 (mtp) cc_final: 0.8395 (mtp) REVERT: E 170 LYS cc_start: 0.8737 (mttt) cc_final: 0.8481 (mtpp) REVERT: K 3 GLN cc_start: 0.8432 (mp10) cc_final: 0.8160 (mp10) REVERT: K 459 ARG cc_start: 0.8167 (pmt-80) cc_final: 0.7822 (ppt170) REVERT: K 472 ASN cc_start: 0.7382 (t0) cc_final: 0.6888 (t0) REVERT: L 482 TYR cc_start: 0.8800 (m-80) cc_final: 0.8234 (m-80) REVERT: M 459 ARG cc_start: 0.8460 (pmt-80) cc_final: 0.7958 (pmt-80) REVERT: M 469 GLU cc_start: 0.8117 (mp0) cc_final: 0.7798 (mp0) REVERT: M 480 VAL cc_start: 0.8771 (t) cc_final: 0.8522 (p) outliers start: 27 outliers final: 23 residues processed: 242 average time/residue: 0.2923 time to fit residues: 106.7635 Evaluate side-chains 243 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain K residue 1 GLN Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 VAL Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 407 LEU 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: 7.9990 chunk 165 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.077640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.052063 restraints weight = 237552.420| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 6.18 r_work: 0.2514 rms_B_bonded: 5.36 restraints_weight: 2.0000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2518 r_free = 0.2518 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17227 Z= 0.346 Angle : 0.614 13.101 23484 Z= 0.306 Chirality : 0.046 0.263 2689 Planarity : 0.003 0.032 2890 Dihedral : 6.542 55.075 2898 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.46 % Allowed : 13.17 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.85 (0.19), residues: 2022 helix: 2.46 (0.22), residues: 573 sheet: 1.15 (0.21), residues: 625 loop : 0.49 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 315 HIS 0.003 0.001 HIS C 107 PHE 0.018 0.002 PHE K 455 TYR 0.026 0.002 TYR B 299 ARG 0.007 0.000 ARG D 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3879.59 seconds wall clock time: 70 minutes 43.41 seconds (4243.41 seconds total)