Starting phenix.real_space_refine on Wed Mar 4 22:28:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qn8_14070/03_2026/7qn8_14070.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qn8_14070/03_2026/7qn8_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/cci-nas-00/data/ceres_data/7qn8_14070/03_2026/7qn8_14070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qn8_14070/03_2026/7qn8_14070.map" model { file = "/net/cci-nas-00/data/ceres_data/7qn8_14070/03_2026/7qn8_14070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qn8_14070/03_2026/7qn8_14070.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 6.25, per 1000 atoms: 0.37 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 - 3.00 Amino acid : True - 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: 1.44 Conformation dependent library (CDL) restraints added in 1.3 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... Secondary structure from input PDB file: 53 helices and 24 sheets defined 35.5% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.531A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.545A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 242 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) removed outlier: 3.572A pdb=" N ILE A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 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 279 through 307 Processing helix chain 'A' and resid 423 through 447 Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.531A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.545A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 242 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) removed outlier: 3.558A pdb=" N ILE B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 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 279 through 307 Processing helix chain 'B' and resid 423 through 447 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.531A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.545A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 242 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) removed outlier: 3.520A pdb=" N ILE C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 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 279 through 307 Processing helix chain 'C' and resid 423 through 447 Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.530A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.544A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 242 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) removed outlier: 3.533A pdb=" N ILE D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 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 279 through 307 Processing helix chain 'D' and resid 423 through 447 Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 112 through 119 removed outlier: 4.089A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 248 through 268 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) Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 275 through 300 Processing helix chain 'E' and resid 308 through 336 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 451 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 495 through 497 No H-bonds generated for 'chain 'K' and resid 495 through 497' Processing helix chain 'L' and resid 495 through 497 No H-bonds generated for 'chain 'L' and resid 495 through 497' Processing helix chain 'M' and resid 495 through 497 No H-bonds generated for 'chain 'M' and resid 495 through 497' Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.514A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, 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) removed outlier: 4.838A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.515A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, 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) removed outlier: 4.838A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA7, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.515A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, 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) removed outlier: 4.838A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, 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=AB1, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.514A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB2, 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) removed outlier: 4.838A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB4, first strand: chain 'E' and resid 109 through 111 removed outlier: 3.582A pdb=" N ILE E 144 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA E 163 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA E 129 " --> pdb=" O ALA E 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 109 through 111 removed outlier: 3.582A pdb=" N ILE E 144 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU E 84 " --> pdb=" O HIS E 77 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N HIS E 77 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) 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) Processing sheet with id=AB6, 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=AB7, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AB8, first strand: chain 'K' and resid 445 through 447 removed outlier: 6.562A pdb=" N TRP K 423 " --> pdb=" O VAL K 435 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA K 437 " --> pdb=" O MET K 421 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET K 421 " --> pdb=" O ALA K 437 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 445 through 447 removed outlier: 6.562A pdb=" N TRP K 423 " --> pdb=" O VAL K 435 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA K 437 " --> pdb=" O MET K 421 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET K 421 " --> pdb=" O ALA K 437 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AC2, first strand: chain 'L' and resid 445 through 447 removed outlier: 6.561A pdb=" N TRP L 423 " --> pdb=" O VAL L 435 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA L 437 " --> pdb=" O MET L 421 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET L 421 " --> pdb=" O ALA L 437 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 445 through 447 removed outlier: 6.561A pdb=" N TRP L 423 " --> pdb=" O VAL L 435 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA L 437 " --> pdb=" O MET L 421 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET L 421 " --> pdb=" O ALA L 437 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AC5, first strand: chain 'M' and resid 445 through 447 removed outlier: 6.561A pdb=" N TRP M 423 " --> pdb=" O VAL M 435 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA M 437 " --> pdb=" O MET M 421 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET M 421 " --> pdb=" O ALA M 437 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 445 through 447 removed outlier: 6.561A pdb=" N TRP M 423 " --> pdb=" O VAL M 435 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA M 437 " --> pdb=" O MET M 421 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET M 421 " --> pdb=" O ALA M 437 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) 964 hydrogen bonds defined for protein. 2726 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: 3.02 Time building geometry restraints manager: 1.98 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: 0.00 - 1.09: 22836 1.09 - 2.17: 432 2.17 - 3.26: 172 3.26 - 4.35: 30 4.35 - 5.43: 14 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: 3115 2.78 - 3.31: 15482 3.31 - 3.84: 28689 3.84 - 4.37: 35214 4.37 - 4.90: 60197 Nonbonded interactions: 142697 Sorted by model distance: nonbonded pdb=" ND2AASN A 41 " pdb=" O ARG A 169 " model vdw 2.247 3.120 nonbonded pdb=" OH TYR E 171 " pdb=" OH TYR E 250 " model vdw 2.256 3.040 nonbonded pdb=" ND2AASN C 41 " pdb=" O ARG C 169 " model vdw 2.274 3.120 nonbonded pdb=" ND2AASN B 41 " pdb=" O ARG B 169 " model vdw 2.275 3.120 nonbonded pdb=" OE2 GLU L 6 " pdb=" N GLY L 505 " model vdw 2.308 3.120 ... (remaining 142692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.410 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.110 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- 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 17264 Z= 0.123 Angle : 0.469 9.202 23587 Z= 0.213 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG C 213 TYR 0.015 0.001 TYR D 66 PHE 0.008 0.001 PHE E 90 TRP 0.005 0.001 TRP B 443 HIS 0.002 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00254 (17227) covalent geometry : angle 0.45634 (23484) SS BOND : bond 0.00048 ( 8) SS BOND : angle 0.38005 ( 16) hydrogen bonds : bond 0.21931 ( 837) hydrogen bonds : angle 7.22593 ( 2726) link_ALPHA1-3 : bond 0.00231 ( 4) link_ALPHA1-3 : angle 1.21405 ( 12) link_ALPHA1-6 : bond 0.00115 ( 4) link_ALPHA1-6 : angle 1.26658 ( 12) link_BETA1-4 : bond 0.00117 ( 12) link_BETA1-4 : angle 1.14103 ( 36) link_NAG-ASN : bond 0.00146 ( 9) link_NAG-ASN : angle 2.73926 ( 27) *********************** 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 to be fit. rotamer outliers: 6 poor density : 415 time to evaluate : 0.607 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: 0.6964 (t0) REVERT: D 52 GLU cc_start: 0.8257 (mp0) cc_final: 0.7990 (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: 0.8068 (m-10) REVERT: L 481 TYR cc_start: 0.7708 (m-80) cc_final: 0.7155 (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: 0.1442 time to fit residues: 88.7213 Evaluate side-chains 242 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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 C 41 ASN B C 64 GLN E 443 ASN K 461 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.085242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059424 restraints weight = 253386.916| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 6.60 r_work: 0.2697 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17264 Z= 0.133 Angle : 0.639 12.692 23587 Z= 0.323 Chirality : 0.046 0.241 2689 Planarity : 0.004 0.046 2890 Dihedral : 8.949 78.465 2899 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.35 % Allowed : 8.61 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 2022 helix: 2.58 (0.21), residues: 577 sheet: 1.05 (0.22), residues: 590 loop : 1.10 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 68 TYR 0.020 0.002 TYR C 244 PHE 0.022 0.002 PHE D 433 TRP 0.015 0.001 TRP E 315 HIS 0.018 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00280 (17227) covalent geometry : angle 0.62718 (23484) SS BOND : bond 0.00949 ( 8) SS BOND : angle 0.97390 ( 16) hydrogen bonds : bond 0.04907 ( 837) hydrogen bonds : angle 5.02871 ( 2726) link_ALPHA1-3 : bond 0.00788 ( 4) link_ALPHA1-3 : angle 2.28914 ( 12) link_ALPHA1-6 : bond 0.00765 ( 4) link_ALPHA1-6 : angle 1.66047 ( 12) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 1.69765 ( 36) link_NAG-ASN : bond 0.00243 ( 9) link_NAG-ASN : angle 2.60916 ( 27) *********************** 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 276 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9014 (mtp) cc_final: 0.8738 (mmm) REVERT: A 224 GLN cc_start: 0.8960 (tp40) cc_final: 0.8624 (tp40) REVERT: A 283 MET cc_start: 0.8604 (mmm) cc_final: 0.8375 (mmt) REVERT: B 243 ASN cc_start: 0.8063 (t0) cc_final: 0.7791 (t0) REVERT: B 306 PHE cc_start: 0.8762 (t80) cc_final: 0.8393 (t80) REVERT: C 224 GLN cc_start: 0.8827 (tp40) cc_final: 0.8440 (tp40) REVERT: C 243 ASN cc_start: 0.7497 (t0) cc_final: 0.6760 (t0) REVERT: C 261 MET cc_start: 0.9367 (mmm) cc_final: 0.9144 (mmm) REVERT: E 83 MET cc_start: 0.9313 (mmm) cc_final: 0.8881 (mmt) REVERT: E 170 LYS cc_start: 0.8628 (mttt) cc_final: 0.8337 (mtpp) REVERT: E 264 MET cc_start: 0.9241 (ttm) cc_final: 0.9010 (ttm) REVERT: K 433 GLU cc_start: 0.7608 (mp0) cc_final: 0.7381 (mp0) REVERT: K 460 ASP cc_start: 0.8089 (t0) cc_final: 0.7857 (t0) REVERT: L 433 GLU cc_start: 0.8695 (tt0) cc_final: 0.8482 (pt0) REVERT: L 460 ASP cc_start: 0.8290 (t0) cc_final: 0.7674 (t0) REVERT: L 474 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8516 (mmmt) REVERT: L 482 TYR cc_start: 0.9065 (m-80) cc_final: 0.8718 (m-80) REVERT: M 425 ARG cc_start: 0.8597 (ptt180) cc_final: 0.8208 (ptt180) REVERT: M 433 GLU cc_start: 0.8578 (tt0) cc_final: 0.8306 (pt0) REVERT: M 482 TYR cc_start: 0.8648 (m-80) cc_final: 0.7666 (m-80) outliers start: 24 outliers final: 10 residues processed: 268 average time/residue: 0.1302 time to fit residues: 53.0646 Evaluate side-chains 229 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU 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 253 LEU 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 L 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 75 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN D 41 ASN E 200 GLN K 461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.082464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056702 restraints weight = 249709.544| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 6.46 r_work: 0.2629 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17264 Z= 0.143 Angle : 0.586 14.946 23587 Z= 0.295 Chirality : 0.045 0.222 2689 Planarity : 0.003 0.041 2890 Dihedral : 8.142 70.577 2897 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.63 % Allowed : 9.45 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.19), residues: 2022 helix: 2.51 (0.21), residues: 577 sheet: 1.12 (0.21), residues: 599 loop : 0.96 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 459 TYR 0.022 0.002 TYR B 299 PHE 0.019 0.002 PHE D 433 TRP 0.013 0.001 TRP E 315 HIS 0.002 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00316 (17227) covalent geometry : angle 0.57688 (23484) SS BOND : bond 0.00204 ( 8) SS BOND : angle 0.90534 ( 16) hydrogen bonds : bond 0.04211 ( 837) hydrogen bonds : angle 4.58367 ( 2726) link_ALPHA1-3 : bond 0.00898 ( 4) link_ALPHA1-3 : angle 1.55934 ( 12) link_ALPHA1-6 : bond 0.00953 ( 4) link_ALPHA1-6 : angle 1.71135 ( 12) link_BETA1-4 : bond 0.00258 ( 12) link_BETA1-4 : angle 1.60948 ( 36) link_NAG-ASN : bond 0.00114 ( 9) link_NAG-ASN : angle 2.13664 ( 27) *********************** 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 270 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8681 (mmm) REVERT: A 224 GLN cc_start: 0.8908 (tp40) cc_final: 0.8566 (tp40) REVERT: B 243 ASN cc_start: 0.8099 (t0) cc_final: 0.7735 (t0) REVERT: B 306 PHE cc_start: 0.8689 (t80) cc_final: 0.7315 (t80) REVERT: C 224 GLN cc_start: 0.8887 (tp40) cc_final: 0.8451 (tp40) REVERT: C 243 ASN cc_start: 0.7533 (t0) cc_final: 0.6838 (t0) REVERT: C 261 MET cc_start: 0.9394 (mmm) cc_final: 0.9149 (mmm) REVERT: D 227 MET cc_start: 0.8677 (mmm) cc_final: 0.8016 (mmm) REVERT: E 83 MET cc_start: 0.9313 (mmm) cc_final: 0.8903 (mmt) REVERT: E 104 HIS cc_start: 0.6670 (OUTLIER) cc_final: 0.6141 (t-90) REVERT: E 170 LYS cc_start: 0.8565 (mttt) cc_final: 0.8308 (mtpp) REVERT: E 179 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8434 (mtp) REVERT: E 264 MET cc_start: 0.9295 (ttm) cc_final: 0.9082 (ttm) REVERT: E 315 TRP cc_start: 0.8031 (m100) cc_final: 0.7762 (m100) REVERT: K 460 ASP cc_start: 0.8023 (t0) cc_final: 0.7711 (t0) REVERT: L 433 GLU cc_start: 0.8673 (tt0) cc_final: 0.8446 (pt0) REVERT: L 460 ASP cc_start: 0.8322 (t0) cc_final: 0.8112 (t0) REVERT: L 472 ASN cc_start: 0.8559 (t0) cc_final: 0.8138 (t0) REVERT: L 474 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8624 (mmmm) REVERT: L 482 TYR cc_start: 0.9072 (m-80) cc_final: 0.8774 (m-80) REVERT: M 455 PHE cc_start: 0.8658 (m-10) cc_final: 0.8305 (m-10) REVERT: M 459 ARG cc_start: 0.8044 (pmt-80) cc_final: 0.7742 (pmt-80) REVERT: M 469 GLU cc_start: 0.8451 (mp0) cc_final: 0.7983 (mp0) REVERT: M 474 LYS cc_start: 0.8569 (mttp) cc_final: 0.8351 (mttp) outliers start: 29 outliers final: 12 residues processed: 254 average time/residue: 0.1252 time to fit residues: 48.4934 Evaluate side-chains 235 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET 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 84 GLU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 179 MET 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 M residue 467 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 14 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 128 optimal weight: 0.3980 chunk 171 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A K 461 ASN M 507 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.056763 restraints weight = 274464.611| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 6.67 r_work: 0.2627 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17264 Z= 0.118 Angle : 0.561 10.499 23587 Z= 0.282 Chirality : 0.044 0.236 2689 Planarity : 0.003 0.037 2890 Dihedral : 7.561 64.780 2897 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.74 % Allowed : 10.30 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.19), residues: 2022 helix: 2.55 (0.21), residues: 578 sheet: 1.03 (0.20), residues: 671 loop : 1.06 (0.24), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 68 TYR 0.021 0.002 TYR B 299 PHE 0.031 0.001 PHE K 455 TRP 0.009 0.001 TRP E 315 HIS 0.002 0.001 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00257 (17227) covalent geometry : angle 0.55176 (23484) SS BOND : bond 0.00249 ( 8) SS BOND : angle 0.63258 ( 16) hydrogen bonds : bond 0.03734 ( 837) hydrogen bonds : angle 4.37491 ( 2726) link_ALPHA1-3 : bond 0.00934 ( 4) link_ALPHA1-3 : angle 1.75910 ( 12) link_ALPHA1-6 : bond 0.00994 ( 4) link_ALPHA1-6 : angle 1.74905 ( 12) link_BETA1-4 : bond 0.00276 ( 12) link_BETA1-4 : angle 1.51743 ( 36) link_NAG-ASN : bond 0.00103 ( 9) link_NAG-ASN : angle 1.98735 ( 27) *********************** 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 263 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 243 ASN cc_start: 0.7865 (t0) cc_final: 0.7604 (t0) REVERT: C 30 ASP cc_start: 0.9087 (m-30) cc_final: 0.8728 (t0) REVERT: C 224 GLN cc_start: 0.8905 (tp40) cc_final: 0.8447 (tp40) REVERT: C 243 ASN cc_start: 0.7537 (t0) cc_final: 0.6829 (t0) REVERT: C 261 MET cc_start: 0.9398 (mmm) cc_final: 0.9129 (mmm) REVERT: D 227 MET cc_start: 0.8454 (mmm) cc_final: 0.7876 (mmm) REVERT: E 104 HIS cc_start: 0.6587 (OUTLIER) cc_final: 0.6087 (t-90) REVERT: E 170 LYS cc_start: 0.8628 (mttt) cc_final: 0.8383 (mtpp) REVERT: E 179 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8428 (mtp) REVERT: E 294 MET cc_start: 0.7662 (ttp) cc_final: 0.7366 (ttp) REVERT: K 1 GLN cc_start: 0.8785 (pm20) cc_final: 0.8399 (pm20) REVERT: K 460 ASP cc_start: 0.7953 (t0) cc_final: 0.7660 (t0) REVERT: L 433 GLU cc_start: 0.8645 (tt0) cc_final: 0.8441 (pt0) REVERT: L 460 ASP cc_start: 0.8336 (t0) cc_final: 0.7697 (t0) REVERT: L 472 ASN cc_start: 0.8625 (t0) cc_final: 0.8260 (t0) REVERT: L 474 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8675 (mmmm) REVERT: L 482 TYR cc_start: 0.9084 (m-80) cc_final: 0.8863 (m-80) REVERT: M 459 ARG cc_start: 0.8192 (pmt-80) cc_final: 0.7816 (pmt-80) REVERT: M 469 GLU cc_start: 0.8451 (mp0) cc_final: 0.7974 (mp0) REVERT: M 474 LYS cc_start: 0.8537 (mttp) cc_final: 0.8302 (mttp) outliers start: 30 outliers final: 18 residues processed: 250 average time/residue: 0.1251 time to fit residues: 47.9931 Evaluate side-chains 236 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL 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 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 84 GLU 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 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 456 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 36 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN K 461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.079903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.054262 restraints weight = 216325.540| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 6.04 r_work: 0.2577 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17264 Z= 0.165 Angle : 0.592 16.334 23587 Z= 0.296 Chirality : 0.045 0.242 2689 Planarity : 0.003 0.036 2890 Dihedral : 7.316 60.550 2897 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.97 % Allowed : 11.54 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.19), residues: 2022 helix: 2.50 (0.21), residues: 578 sheet: 1.24 (0.21), residues: 599 loop : 0.77 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 141 TYR 0.023 0.002 TYR D 299 PHE 0.024 0.002 PHE B 306 TRP 0.019 0.001 TRP E 315 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00371 (17227) covalent geometry : angle 0.58221 (23484) SS BOND : bond 0.00205 ( 8) SS BOND : angle 1.05285 ( 16) hydrogen bonds : bond 0.03737 ( 837) hydrogen bonds : angle 4.36150 ( 2726) link_ALPHA1-3 : bond 0.00756 ( 4) link_ALPHA1-3 : angle 1.83212 ( 12) link_ALPHA1-6 : bond 0.00944 ( 4) link_ALPHA1-6 : angle 1.73984 ( 12) link_BETA1-4 : bond 0.00248 ( 12) link_BETA1-4 : angle 1.70999 ( 36) link_NAG-ASN : bond 0.00128 ( 9) link_NAG-ASN : angle 1.95453 ( 27) *********************** 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 265 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 243 ASN cc_start: 0.7986 (t0) cc_final: 0.7732 (t0) REVERT: C 30 ASP cc_start: 0.9081 (m-30) cc_final: 0.8762 (t0) REVERT: C 224 GLN cc_start: 0.8924 (tp40) cc_final: 0.8454 (tp40) REVERT: C 243 ASN cc_start: 0.7649 (t0) cc_final: 0.6930 (t0) REVERT: C 261 MET cc_start: 0.9431 (mmm) cc_final: 0.9168 (mmm) REVERT: D 227 MET cc_start: 0.8500 (mmm) cc_final: 0.7901 (mmm) REVERT: D 283 MET cc_start: 0.9131 (mtp) cc_final: 0.8854 (mtt) REVERT: E 104 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.6259 (t-90) REVERT: E 170 LYS cc_start: 0.8669 (mttt) cc_final: 0.8426 (mtpp) REVERT: E 179 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8517 (mtp) REVERT: E 226 MET cc_start: 0.8099 (mmm) cc_final: 0.7890 (mmm) REVERT: E 260 LEU cc_start: 0.9132 (pp) cc_final: 0.8792 (mt) REVERT: K 459 ARG cc_start: 0.8426 (pmt-80) cc_final: 0.7957 (ppt170) REVERT: K 460 ASP cc_start: 0.7945 (t0) cc_final: 0.7604 (t0) REVERT: K 469 GLU cc_start: 0.8111 (mp0) cc_final: 0.7394 (mp0) REVERT: K 504 GLN cc_start: 0.8532 (mp10) cc_final: 0.8258 (pm20) REVERT: L 433 GLU cc_start: 0.8627 (tt0) cc_final: 0.8416 (pt0) REVERT: L 472 ASN cc_start: 0.8651 (t0) cc_final: 0.8269 (t0) REVERT: L 474 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8648 (mmmm) REVERT: L 482 TYR cc_start: 0.9105 (m-80) cc_final: 0.8774 (m-80) REVERT: M 459 ARG cc_start: 0.8416 (pmt-80) cc_final: 0.8043 (pmt-80) REVERT: M 469 GLU cc_start: 0.8482 (mp0) cc_final: 0.7983 (mp0) REVERT: M 474 LYS cc_start: 0.8479 (mttp) cc_final: 0.8252 (mttp) outliers start: 34 outliers final: 21 residues processed: 249 average time/residue: 0.1184 time to fit residues: 45.7991 Evaluate side-chains 246 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET 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 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 165 GLU Chi-restraints excluded: chain D residue 253 LEU 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 179 MET 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 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 1 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 461 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.078554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.052959 restraints weight = 239253.846| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 6.18 r_work: 0.2550 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17264 Z= 0.180 Angle : 0.585 13.939 23587 Z= 0.295 Chirality : 0.045 0.245 2689 Planarity : 0.003 0.035 2890 Dihedral : 7.168 57.457 2897 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.03 % Allowed : 11.54 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.19), residues: 2022 helix: 2.48 (0.21), residues: 582 sheet: 1.14 (0.21), residues: 647 loop : 0.69 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 141 TYR 0.025 0.002 TYR B 299 PHE 0.027 0.002 PHE K 455 TRP 0.017 0.001 TRP E 315 HIS 0.003 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00409 (17227) covalent geometry : angle 0.57512 (23484) SS BOND : bond 0.00209 ( 8) SS BOND : angle 0.99392 ( 16) hydrogen bonds : bond 0.03746 ( 837) hydrogen bonds : angle 4.34077 ( 2726) link_ALPHA1-3 : bond 0.00773 ( 4) link_ALPHA1-3 : angle 1.76038 ( 12) link_ALPHA1-6 : bond 0.00943 ( 4) link_ALPHA1-6 : angle 1.67763 ( 12) link_BETA1-4 : bond 0.00251 ( 12) link_BETA1-4 : angle 1.71895 ( 36) link_NAG-ASN : bond 0.00102 ( 9) link_NAG-ASN : angle 1.90485 ( 27) *********************** 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 266 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 95 ASP cc_start: 0.9038 (p0) cc_final: 0.8744 (p0) REVERT: A 265 ASN cc_start: 0.8082 (t0) cc_final: 0.7781 (t0) REVERT: A 286 MET cc_start: 0.8298 (mmp) cc_final: 0.7343 (mtt) REVERT: B 49 MET cc_start: 0.8865 (ptm) cc_final: 0.8461 (ppp) REVERT: B 243 ASN cc_start: 0.8094 (t0) cc_final: 0.7872 (t0) REVERT: C 30 ASP cc_start: 0.9070 (m-30) cc_final: 0.8769 (t0) REVERT: C 224 GLN cc_start: 0.8940 (tp40) cc_final: 0.8446 (tp40) REVERT: C 243 ASN cc_start: 0.7728 (t0) cc_final: 0.7026 (t0) REVERT: D 227 MET cc_start: 0.8468 (mmm) cc_final: 0.7860 (mmm) REVERT: D 283 MET cc_start: 0.9088 (mtp) cc_final: 0.8833 (mtt) REVERT: E 83 MET cc_start: 0.9366 (mmt) cc_final: 0.9086 (mmt) REVERT: E 104 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.6244 (t-90) REVERT: E 170 LYS cc_start: 0.8717 (mttt) cc_final: 0.8463 (mtpp) REVERT: E 179 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8499 (mtp) REVERT: K 1 GLN cc_start: 0.8644 (pm20) cc_final: 0.8290 (pm20) REVERT: K 3 GLN cc_start: 0.8387 (mp10) cc_final: 0.8100 (mp10) REVERT: K 459 ARG cc_start: 0.8454 (pmt-80) cc_final: 0.8038 (ppt170) REVERT: K 460 ASP cc_start: 0.8038 (t0) cc_final: 0.7726 (t0) REVERT: K 461 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8050 (t0) REVERT: K 464 ASN cc_start: 0.8720 (m110) cc_final: 0.8440 (m-40) REVERT: K 469 GLU cc_start: 0.8290 (mp0) cc_final: 0.7928 (mp0) REVERT: K 470 MET cc_start: 0.8398 (mtm) cc_final: 0.7697 (mpp) REVERT: L 433 GLU cc_start: 0.8580 (tt0) cc_final: 0.8371 (pt0) REVERT: L 472 ASN cc_start: 0.8692 (t0) cc_final: 0.8342 (t0) REVERT: L 474 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8683 (mmmm) REVERT: L 482 TYR cc_start: 0.9137 (m-80) cc_final: 0.8755 (m-80) REVERT: M 459 ARG cc_start: 0.8517 (pmt-80) cc_final: 0.8066 (pmt-80) REVERT: M 460 ASP cc_start: 0.8249 (t70) cc_final: 0.7463 (p0) REVERT: M 469 GLU cc_start: 0.8438 (mp0) cc_final: 0.7823 (mp0) REVERT: M 474 LYS cc_start: 0.8442 (mttp) cc_final: 0.8223 (mttp) outliers start: 34 outliers final: 21 residues processed: 247 average time/residue: 0.1248 time to fit residues: 47.4664 Evaluate side-chains 244 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET 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 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 165 GLU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 84 GLU 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 441 SER Chi-restraints excluded: chain K residue 451 VAL Chi-restraints excluded: chain K residue 456 THR Chi-restraints excluded: chain K residue 461 ASN 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 467 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 chunk 169 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.079733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.054219 restraints weight = 237367.685| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 6.18 r_work: 0.2575 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17264 Z= 0.113 Angle : 0.567 13.136 23587 Z= 0.280 Chirality : 0.044 0.242 2689 Planarity : 0.003 0.037 2890 Dihedral : 6.756 56.131 2897 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.63 % Allowed : 12.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 2022 helix: 2.52 (0.21), residues: 579 sheet: 1.20 (0.20), residues: 644 loop : 0.75 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 141 TYR 0.022 0.001 TYR B 299 PHE 0.018 0.001 PHE C 433 TRP 0.018 0.001 TRP E 315 HIS 0.002 0.000 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00245 (17227) covalent geometry : angle 0.55950 (23484) SS BOND : bond 0.00160 ( 8) SS BOND : angle 0.75417 ( 16) hydrogen bonds : bond 0.03494 ( 837) hydrogen bonds : angle 4.21069 ( 2726) link_ALPHA1-3 : bond 0.00882 ( 4) link_ALPHA1-3 : angle 1.58782 ( 12) link_ALPHA1-6 : bond 0.01033 ( 4) link_ALPHA1-6 : angle 1.58579 ( 12) link_BETA1-4 : bond 0.00267 ( 12) link_BETA1-4 : angle 1.52645 ( 36) link_NAG-ASN : bond 0.00089 ( 9) link_NAG-ASN : angle 1.77822 ( 27) *********************** 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 260 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8243 (mmm) REVERT: A 95 ASP cc_start: 0.9047 (p0) cc_final: 0.8772 (p0) REVERT: A 265 ASN cc_start: 0.8149 (t0) cc_final: 0.7873 (t0) REVERT: A 286 MET cc_start: 0.8313 (mmp) cc_final: 0.7364 (mtt) REVERT: B 49 MET cc_start: 0.8891 (ptm) cc_final: 0.8535 (ppp) REVERT: B 66 TYR cc_start: 0.8777 (m-80) cc_final: 0.8562 (m-80) REVERT: B 243 ASN cc_start: 0.8096 (t0) cc_final: 0.7876 (t0) REVERT: C 30 ASP cc_start: 0.9056 (m-30) cc_final: 0.8751 (t0) REVERT: C 224 GLN cc_start: 0.8911 (tp40) cc_final: 0.8660 (tp40) REVERT: C 243 ASN cc_start: 0.7703 (t0) cc_final: 0.6996 (t0) REVERT: D 227 MET cc_start: 0.8417 (mmm) cc_final: 0.7833 (mmm) REVERT: D 283 MET cc_start: 0.9128 (mtp) cc_final: 0.8881 (mtt) REVERT: D 437 LEU cc_start: 0.8628 (tt) cc_final: 0.8176 (mp) REVERT: E 83 MET cc_start: 0.9390 (mmt) cc_final: 0.9122 (mmt) REVERT: E 104 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6225 (t-90) REVERT: E 170 LYS cc_start: 0.8710 (mttt) cc_final: 0.8459 (mtpp) REVERT: E 179 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8503 (mtp) REVERT: K 1 GLN cc_start: 0.8624 (pm20) cc_final: 0.8257 (pm20) REVERT: K 459 ARG cc_start: 0.8417 (pmt-80) cc_final: 0.7891 (ppt170) REVERT: K 464 ASN cc_start: 0.8769 (m110) cc_final: 0.8486 (m-40) REVERT: K 469 GLU cc_start: 0.8288 (mp0) cc_final: 0.7712 (mp0) REVERT: K 474 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8021 (mmtt) REVERT: L 426 GLN cc_start: 0.9008 (tt0) cc_final: 0.8680 (tp40) REVERT: L 433 GLU cc_start: 0.8557 (tt0) cc_final: 0.8353 (pt0) REVERT: L 472 ASN cc_start: 0.8678 (t0) cc_final: 0.8350 (t0) REVERT: L 474 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8725 (mmmm) REVERT: L 482 TYR cc_start: 0.9136 (m-80) cc_final: 0.8743 (m-80) REVERT: M 459 ARG cc_start: 0.8580 (pmt-80) cc_final: 0.8116 (pmt-80) REVERT: M 460 ASP cc_start: 0.8302 (t70) cc_final: 0.7656 (p0) REVERT: M 469 GLU cc_start: 0.8429 (mp0) cc_final: 0.7820 (mp0) REVERT: M 474 LYS cc_start: 0.8376 (mttp) cc_final: 0.8164 (mttp) outliers start: 27 outliers final: 21 residues processed: 246 average time/residue: 0.1252 time to fit residues: 47.4449 Evaluate side-chains 251 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET 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 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 268 LEU 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 179 MET 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 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 124 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN D 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.078682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.052976 restraints weight = 233537.862| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 6.15 r_work: 0.2549 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 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 0.031 17264 Z= 0.159 Angle : 0.580 13.041 23587 Z= 0.289 Chirality : 0.044 0.251 2689 Planarity : 0.003 0.028 2890 Dihedral : 6.687 55.350 2897 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.86 % Allowed : 12.10 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.19), residues: 2022 helix: 2.50 (0.21), residues: 579 sheet: 1.18 (0.20), residues: 647 loop : 0.69 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.025 0.002 TYR B 299 PHE 0.016 0.001 PHE C 433 TRP 0.024 0.001 TRP E 315 HIS 0.002 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00359 (17227) covalent geometry : angle 0.57113 (23484) SS BOND : bond 0.00164 ( 8) SS BOND : angle 0.94736 ( 16) hydrogen bonds : bond 0.03557 ( 837) hydrogen bonds : angle 4.26835 ( 2726) link_ALPHA1-3 : bond 0.00765 ( 4) link_ALPHA1-3 : angle 1.78243 ( 12) link_ALPHA1-6 : bond 0.00972 ( 4) link_ALPHA1-6 : angle 1.58006 ( 12) link_BETA1-4 : bond 0.00276 ( 12) link_BETA1-4 : angle 1.67207 ( 36) link_NAG-ASN : bond 0.00081 ( 9) link_NAG-ASN : angle 1.83730 ( 27) *********************** 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 263 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 55 MET cc_start: 0.9092 (mmt) cc_final: 0.8628 (mmm) REVERT: A 95 ASP cc_start: 0.9039 (p0) cc_final: 0.8742 (p0) REVERT: A 265 ASN cc_start: 0.8127 (t0) cc_final: 0.7877 (t0) REVERT: A 286 MET cc_start: 0.8300 (mmp) cc_final: 0.7367 (mtt) REVERT: B 49 MET cc_start: 0.8910 (ptm) cc_final: 0.8549 (ppp) REVERT: B 243 ASN cc_start: 0.8104 (t0) cc_final: 0.7880 (t0) REVERT: C 30 ASP cc_start: 0.9057 (m-30) cc_final: 0.8777 (t0) REVERT: C 224 GLN cc_start: 0.8927 (tp40) cc_final: 0.8669 (tp40) REVERT: C 243 ASN cc_start: 0.7742 (t0) cc_final: 0.7033 (t0) REVERT: D 141 ARG cc_start: 0.9033 (mtt90) cc_final: 0.8761 (mtt90) REVERT: D 227 MET cc_start: 0.8482 (mmm) cc_final: 0.7912 (mmm) REVERT: D 270 GLU cc_start: 0.8686 (pt0) cc_final: 0.8448 (pp20) REVERT: D 283 MET cc_start: 0.9133 (mtp) cc_final: 0.8907 (mtt) REVERT: D 437 LEU cc_start: 0.8631 (tt) cc_final: 0.8161 (mp) REVERT: E 83 MET cc_start: 0.9387 (mmt) cc_final: 0.9107 (mmt) REVERT: E 104 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.6236 (t-90) REVERT: E 170 LYS cc_start: 0.8732 (mttt) cc_final: 0.8480 (mtpp) REVERT: E 179 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8499 (mtp) REVERT: E 260 LEU cc_start: 0.9092 (pp) cc_final: 0.8780 (mt) REVERT: K 1 GLN cc_start: 0.8669 (pm20) cc_final: 0.8316 (pm20) REVERT: K 3 GLN cc_start: 0.8428 (mp10) cc_final: 0.8132 (mp10) REVERT: K 459 ARG cc_start: 0.8599 (pmt-80) cc_final: 0.7966 (ppt170) REVERT: K 469 GLU cc_start: 0.8288 (mp0) cc_final: 0.7758 (mp0) REVERT: K 474 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7940 (mmtt) REVERT: L 426 GLN cc_start: 0.9047 (tt0) cc_final: 0.8715 (tp40) REVERT: L 433 GLU cc_start: 0.8593 (tt0) cc_final: 0.8391 (pt0) REVERT: L 472 ASN cc_start: 0.8699 (t0) cc_final: 0.8412 (t0) REVERT: L 474 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8653 (mmmm) REVERT: L 482 TYR cc_start: 0.9168 (m-80) cc_final: 0.8711 (m-80) REVERT: M 459 ARG cc_start: 0.8595 (pmt-80) cc_final: 0.8128 (pmt-80) REVERT: M 460 ASP cc_start: 0.8281 (t70) cc_final: 0.7733 (p0) REVERT: M 469 GLU cc_start: 0.8496 (mp0) cc_final: 0.7795 (mp0) outliers start: 31 outliers final: 27 residues processed: 245 average time/residue: 0.1280 time to fit residues: 48.0399 Evaluate side-chains 254 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET 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 64 GLN 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 218 ILE Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 268 LEU 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 179 MET 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 466 VAL Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR 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 188 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 303 ASN C 41 ASN B D 224 GLN ** L 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.052313 restraints weight = 248265.585| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 6.24 r_work: 0.2524 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17264 Z= 0.204 Angle : 0.614 13.416 23587 Z= 0.306 Chirality : 0.045 0.254 2689 Planarity : 0.003 0.029 2890 Dihedral : 6.785 55.036 2897 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.80 % Allowed : 12.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 2022 helix: 2.49 (0.21), residues: 579 sheet: 1.15 (0.20), residues: 647 loop : 0.61 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 141 TYR 0.025 0.002 TYR B 299 PHE 0.016 0.002 PHE C 433 TRP 0.025 0.001 TRP E 315 HIS 0.003 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00466 (17227) covalent geometry : angle 0.60570 (23484) SS BOND : bond 0.00168 ( 8) SS BOND : angle 1.07088 ( 16) hydrogen bonds : bond 0.03685 ( 837) hydrogen bonds : angle 4.36223 ( 2726) link_ALPHA1-3 : bond 0.00726 ( 4) link_ALPHA1-3 : angle 1.75686 ( 12) link_ALPHA1-6 : bond 0.00884 ( 4) link_ALPHA1-6 : angle 1.58621 ( 12) link_BETA1-4 : bond 0.00279 ( 12) link_BETA1-4 : angle 1.77181 ( 36) link_NAG-ASN : bond 0.00163 ( 9) link_NAG-ASN : angle 1.84794 ( 27) *********************** 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 255 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 55 MET cc_start: 0.9097 (mmt) cc_final: 0.8652 (mmm) REVERT: A 95 ASP cc_start: 0.9055 (p0) cc_final: 0.8723 (p0) REVERT: A 265 ASN cc_start: 0.8145 (t0) cc_final: 0.7923 (t0) REVERT: A 286 MET cc_start: 0.8306 (mmp) cc_final: 0.7377 (mtt) REVERT: B 49 MET cc_start: 0.8937 (ptm) cc_final: 0.8579 (ppp) REVERT: B 243 ASN cc_start: 0.8133 (t0) cc_final: 0.7906 (t0) REVERT: C 30 ASP cc_start: 0.9060 (m-30) cc_final: 0.8781 (t0) REVERT: C 224 GLN cc_start: 0.8918 (tp40) cc_final: 0.8657 (tp40) REVERT: C 243 ASN cc_start: 0.7798 (t0) cc_final: 0.7089 (t0) REVERT: D 270 GLU cc_start: 0.8692 (pt0) cc_final: 0.8453 (pp20) REVERT: D 283 MET cc_start: 0.9141 (mtp) cc_final: 0.8913 (mtt) REVERT: E 83 MET cc_start: 0.9376 (mmt) cc_final: 0.9085 (mmt) REVERT: E 104 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.6307 (t-90) REVERT: E 170 LYS cc_start: 0.8720 (mttt) cc_final: 0.8466 (mtpp) REVERT: E 179 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8546 (mtp) REVERT: K 1 GLN cc_start: 0.8694 (pm20) cc_final: 0.8335 (pm20) REVERT: K 3 GLN cc_start: 0.8489 (mp10) cc_final: 0.8182 (mp10) REVERT: K 459 ARG cc_start: 0.8608 (pmt-80) cc_final: 0.8088 (ppt170) REVERT: K 469 GLU cc_start: 0.8274 (mp0) cc_final: 0.7730 (mp0) REVERT: K 474 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8066 (mmtt) REVERT: L 426 GLN cc_start: 0.9012 (tt0) cc_final: 0.8729 (tp40) REVERT: L 433 GLU cc_start: 0.8567 (tt0) cc_final: 0.8363 (pt0) REVERT: L 472 ASN cc_start: 0.8725 (t0) cc_final: 0.8387 (t0) REVERT: L 474 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8716 (mmmm) REVERT: L 482 TYR cc_start: 0.9167 (m-80) cc_final: 0.8671 (m-80) REVERT: M 3 GLN cc_start: 0.8351 (mp10) cc_final: 0.8095 (mp10) REVERT: M 459 ARG cc_start: 0.8607 (pmt-80) cc_final: 0.8151 (pmt-80) REVERT: M 460 ASP cc_start: 0.8290 (t70) cc_final: 0.7774 (p0) REVERT: M 469 GLU cc_start: 0.8455 (mp0) cc_final: 0.8253 (mp0) outliers start: 30 outliers final: 25 residues processed: 238 average time/residue: 0.1281 time to fit residues: 46.4189 Evaluate side-chains 249 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET 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 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 218 ILE Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 426 TRP 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 179 MET 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 K residue 480 VAL Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 51 optimal weight: 0.0010 chunk 91 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS D 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.052615 restraints weight = 244612.388| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 6.26 r_work: 0.2538 rms_B_bonded: 5.46 restraints_weight: 2.0000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17264 Z= 0.152 Angle : 0.601 13.355 23587 Z= 0.297 Chirality : 0.044 0.250 2689 Planarity : 0.003 0.039 2890 Dihedral : 6.597 55.402 2897 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.19), residues: 2022 helix: 2.51 (0.21), residues: 579 sheet: 1.27 (0.21), residues: 623 loop : 0.55 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 141 TYR 0.025 0.002 TYR E 318 PHE 0.016 0.001 PHE C 433 TRP 0.027 0.001 TRP E 315 HIS 0.002 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00341 (17227) covalent geometry : angle 0.59325 (23484) SS BOND : bond 0.00158 ( 8) SS BOND : angle 0.82458 ( 16) hydrogen bonds : bond 0.03566 ( 837) hydrogen bonds : angle 4.29623 ( 2726) link_ALPHA1-3 : bond 0.00838 ( 4) link_ALPHA1-3 : angle 1.63156 ( 12) link_ALPHA1-6 : bond 0.00975 ( 4) link_ALPHA1-6 : angle 1.53221 ( 12) link_BETA1-4 : bond 0.00264 ( 12) link_BETA1-4 : angle 1.64734 ( 36) link_NAG-ASN : bond 0.00055 ( 9) link_NAG-ASN : angle 1.75510 ( 27) ********************** 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 254 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8308 (mmm) REVERT: A 95 ASP cc_start: 0.9060 (p0) cc_final: 0.8782 (p0) REVERT: A 286 MET cc_start: 0.8295 (mmp) cc_final: 0.7400 (mtt) REVERT: B 49 MET cc_start: 0.8940 (ptm) cc_final: 0.8591 (ppp) REVERT: B 243 ASN cc_start: 0.8116 (t0) cc_final: 0.7894 (t0) REVERT: C 30 ASP cc_start: 0.9059 (m-30) cc_final: 0.8789 (t0) REVERT: C 224 GLN cc_start: 0.8914 (tp40) cc_final: 0.8663 (tp40) REVERT: C 243 ASN cc_start: 0.7802 (t0) cc_final: 0.7089 (t0) REVERT: D 270 GLU cc_start: 0.8678 (pt0) cc_final: 0.8440 (pp20) REVERT: D 283 MET cc_start: 0.9147 (mtp) cc_final: 0.8931 (mtt) REVERT: D 437 LEU cc_start: 0.8631 (tt) cc_final: 0.8176 (mp) REVERT: E 83 MET cc_start: 0.9399 (mmt) cc_final: 0.9126 (mmt) REVERT: E 104 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.6258 (t-90) REVERT: E 170 LYS cc_start: 0.8751 (mttt) cc_final: 0.8494 (mtpp) REVERT: E 179 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8526 (mtp) REVERT: E 260 LEU cc_start: 0.9094 (pp) cc_final: 0.8798 (mt) REVERT: K 1 GLN cc_start: 0.8690 (pm20) cc_final: 0.8353 (pm20) REVERT: K 3 GLN cc_start: 0.8488 (mp10) cc_final: 0.8173 (mp10) REVERT: K 459 ARG cc_start: 0.8614 (pmt-80) cc_final: 0.8139 (ppt170) REVERT: K 469 GLU cc_start: 0.8296 (mp0) cc_final: 0.7755 (mp0) REVERT: K 474 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8125 (mmtt) REVERT: L 426 GLN cc_start: 0.8978 (tt0) cc_final: 0.8734 (tp40) REVERT: L 472 ASN cc_start: 0.8724 (t0) cc_final: 0.8402 (t0) REVERT: L 474 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8697 (mmmm) REVERT: L 482 TYR cc_start: 0.9166 (m-80) cc_final: 0.8679 (m-80) REVERT: M 3 GLN cc_start: 0.8396 (mp10) cc_final: 0.8128 (mp10) REVERT: M 459 ARG cc_start: 0.8592 (pmt-80) cc_final: 0.8136 (pmt-80) REVERT: M 460 ASP cc_start: 0.8316 (t70) cc_final: 0.7808 (p0) outliers start: 28 outliers final: 24 residues processed: 238 average time/residue: 0.1294 time to fit residues: 47.2152 Evaluate side-chains 251 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 294 LEU 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 218 ILE Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 426 TRP 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 179 MET 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 K residue 480 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 M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 185 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 267 HIS D 224 GLN ** L 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.076891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.051384 restraints weight = 249978.585| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 6.21 r_work: 0.2505 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17264 Z= 0.242 Angle : 0.644 14.229 23587 Z= 0.322 Chirality : 0.046 0.256 2689 Planarity : 0.004 0.036 2890 Dihedral : 6.861 54.491 2897 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.58 % Allowed : 12.83 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.19), residues: 2022 helix: 2.49 (0.21), residues: 574 sheet: 1.19 (0.20), residues: 623 loop : 0.44 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 141 TYR 0.027 0.002 TYR B 299 PHE 0.017 0.002 PHE L 434 TRP 0.031 0.001 TRP E 315 HIS 0.003 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00554 (17227) covalent geometry : angle 0.63543 (23484) SS BOND : bond 0.00183 ( 8) SS BOND : angle 1.18026 ( 16) hydrogen bonds : bond 0.03816 ( 837) hydrogen bonds : angle 4.46165 ( 2726) link_ALPHA1-3 : bond 0.00691 ( 4) link_ALPHA1-3 : angle 1.80835 ( 12) link_ALPHA1-6 : bond 0.00832 ( 4) link_ALPHA1-6 : angle 1.55179 ( 12) link_BETA1-4 : bond 0.00305 ( 12) link_BETA1-4 : angle 1.87919 ( 36) link_NAG-ASN : bond 0.00260 ( 9) link_NAG-ASN : angle 1.86963 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4604.17 seconds wall clock time: 79 minutes 22.79 seconds (4762.79 seconds total)