Starting phenix.real_space_refine on Sun Jun 15 04:12:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qn8_14070/06_2025/7qn8_14070.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qn8_14070/06_2025/7qn8_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_14070/06_2025/7qn8_14070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qn8_14070/06_2025/7qn8_14070.map" model { file = "/net/cci-nas-00/data/ceres_data/7qn8_14070/06_2025/7qn8_14070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qn8_14070/06_2025/7qn8_14070.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 89 5.16 5 C 10897 2.51 5 N 2698 2.21 5 O 3071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16755 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2749 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2683 Chain: "B" Number of atoms: 2753 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2678 Chain: "C" Number of atoms: 2754 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2677 Chain: "D" Number of atoms: 2716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2721 Chain: "E" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2569 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} Chain breaks: 1 Chain: "K" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'HSM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N ALEU A 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 125 " occ=0.50 residue: pdb=" N ASER A 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 209 " occ=0.50 residue: pdb=" N ALEU A 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 214 " occ=0.50 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N ASER B 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 209 " occ=0.50 residue: pdb=" N ALEU B 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 214 " occ=0.50 residue: pdb=" N ASER B 229 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 229 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N ATYR C 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 66 " occ=0.50 residue: pdb=" N ALEU C 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 125 " occ=0.50 residue: pdb=" N ASER C 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 209 " occ=0.50 residue: pdb=" N ASER D 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 209 " occ=0.50 Time building chain proxies: 14.28, per 1000 atoms: 0.85 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: 4.65 Conformation dependent library (CDL) restraints added in 3.3 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: 2.69 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: 5.37 Time building geometry restraints manager: 5.09 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: 1.000 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: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 45.640 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 2022 helix: 2.51 (0.21), residues: 551 sheet: 1.35 (0.22), residues: 630 loop : 0.99 (0.23), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 443 HIS 0.002 0.001 HIS D 267 PHE 0.008 0.001 PHE E 90 TYR 0.015 0.001 TYR D 66 ARG 0.002 0.000 ARG C 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 9) link_NAG-ASN : angle 2.73926 ( 27) 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_ALPHA1-3 : bond 0.00231 ( 4) link_ALPHA1-3 : angle 1.21405 ( 12) hydrogen bonds : bond 0.21931 ( 837) hydrogen bonds : angle 7.22593 ( 2726) SS BOND : bond 0.00048 ( 8) SS BOND : angle 0.38005 ( 16) covalent geometry : bond 0.00254 (17227) covalent geometry : angle 0.45634 (23484) *********************** 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 : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8470 (tttp) cc_final: 0.8113 (tttp) REVERT: A 224 GLN cc_start: 0.8499 (tp40) cc_final: 0.8211 (tp40) REVERT: A 283 MET cc_start: 0.8438 (mmm) cc_final: 0.8226 (mmt) REVERT: A 298 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 157 TYR cc_start: 0.8862 (t80) cc_final: 0.8572 (t80) REVERT: B 215 LYS cc_start: 0.8874 (tttt) cc_final: 0.8648 (ttmm) REVERT: B 243 ASN cc_start: 0.7795 (t0) cc_final: 0.7589 (t0) REVERT: B 306 PHE cc_start: 0.8334 (t80) cc_final: 0.8020 (t80) REVERT: C 224 GLN cc_start: 0.8580 (tp40) cc_final: 0.8268 (tp40) REVERT: C 243 ASN cc_start: 0.7572 (t0) cc_final: 0.6923 (t0) REVERT: D 52 GLU cc_start: 0.8257 (mp0) cc_final: 0.7992 (mp0) REVERT: E 80 GLU cc_start: 0.8251 (pm20) cc_final: 0.8020 (mp0) REVERT: E 83 MET cc_start: 0.9073 (mmm) cc_final: 0.8690 (mmt) REVERT: E 118 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8582 (mppt) REVERT: E 170 LYS cc_start: 0.8615 (mttt) cc_final: 0.8393 (mtpp) REVERT: E 173 MET cc_start: 0.8398 (mpp) cc_final: 0.8166 (mpp) REVERT: E 210 GLN cc_start: 0.8517 (mt0) cc_final: 0.8192 (mt0) REVERT: E 253 GLN cc_start: 0.7181 (tt0) cc_final: 0.6780 (tm-30) REVERT: K 414 HIS cc_start: 0.7084 (m90) cc_final: 0.6749 (m170) REVERT: K 470 MET cc_start: 0.8109 (mtm) cc_final: 0.6996 (mtm) REVERT: K 481 TYR cc_start: 0.5826 (m-80) cc_final: 0.3814 (m-10) REVERT: L 455 PHE cc_start: 0.8373 (m-10) cc_final: 0.8072 (m-10) REVERT: L 481 TYR cc_start: 0.7708 (m-80) cc_final: 0.7158 (m-80) REVERT: M 455 PHE cc_start: 0.8272 (m-10) cc_final: 0.7877 (m-10) REVERT: M 474 LYS cc_start: 0.9025 (mttt) cc_final: 0.8304 (mttp) outliers start: 6 outliers final: 3 residues processed: 421 average time/residue: 0.3140 time to fit residues: 191.4245 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 : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 228 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 D 41 ASN E 443 ASN K 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.082629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.056640 restraints weight = 251535.912| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 6.50 r_work: 0.2630 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17264 Z= 0.183 Angle : 0.663 12.716 23587 Z= 0.336 Chirality : 0.046 0.221 2689 Planarity : 0.004 0.046 2890 Dihedral : 9.028 78.089 2899 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.58 % Allowed : 8.55 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.19), residues: 2022 helix: 2.59 (0.21), residues: 571 sheet: 1.04 (0.22), residues: 590 loop : 1.00 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 315 HIS 0.019 0.001 HIS B 267 PHE 0.023 0.002 PHE D 433 TYR 0.023 0.002 TYR D 66 ARG 0.008 0.001 ARG D 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 9) link_NAG-ASN : angle 2.93484 ( 27) link_ALPHA1-6 : bond 0.00914 ( 4) link_ALPHA1-6 : angle 1.75226 ( 12) link_BETA1-4 : bond 0.00321 ( 12) link_BETA1-4 : angle 1.92241 ( 36) link_ALPHA1-3 : bond 0.00590 ( 4) link_ALPHA1-3 : angle 2.18763 ( 12) hydrogen bonds : bond 0.04917 ( 837) hydrogen bonds : angle 5.04421 ( 2726) SS BOND : bond 0.00763 ( 8) SS BOND : angle 1.04073 ( 16) covalent geometry : bond 0.00411 (17227) covalent geometry : angle 0.64904 (23484) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9066 (mtp) cc_final: 0.8733 (mmm) REVERT: A 224 GLN cc_start: 0.8944 (tp40) cc_final: 0.8586 (tp40) REVERT: A 283 MET cc_start: 0.8633 (mmm) cc_final: 0.8357 (mmt) REVERT: B 243 ASN cc_start: 0.8099 (t0) cc_final: 0.7828 (t0) REVERT: B 306 PHE cc_start: 0.8761 (t80) cc_final: 0.8383 (t80) REVERT: C 224 GLN cc_start: 0.8859 (tp40) cc_final: 0.8480 (tp40) REVERT: C 243 ASN cc_start: 0.7587 (t0) cc_final: 0.6883 (t0) REVERT: C 261 MET cc_start: 0.9379 (mmm) cc_final: 0.9150 (mmm) REVERT: D 227 MET cc_start: 0.8928 (mmm) cc_final: 0.8573 (mmm) REVERT: E 170 LYS cc_start: 0.8645 (mttt) cc_final: 0.8356 (mtpp) REVERT: E 264 MET cc_start: 0.9241 (ttm) cc_final: 0.9011 (ttm) REVERT: K 433 GLU cc_start: 0.7702 (mp0) cc_final: 0.7484 (mp0) REVERT: K 460 ASP cc_start: 0.8110 (t0) cc_final: 0.7892 (t0) REVERT: L 433 GLU cc_start: 0.8678 (tt0) cc_final: 0.8468 (pt0) REVERT: L 460 ASP cc_start: 0.8424 (t0) cc_final: 0.7818 (t0) REVERT: L 474 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8538 (mmmt) REVERT: L 482 TYR cc_start: 0.9111 (m-80) cc_final: 0.8728 (m-80) REVERT: M 466 VAL cc_start: 0.9319 (t) cc_final: 0.9054 (m) REVERT: M 482 TYR cc_start: 0.8691 (m-80) cc_final: 0.7505 (m-80) outliers start: 28 outliers final: 11 residues processed: 265 average time/residue: 0.2795 time to fit residues: 113.3429 Evaluate side-chains 229 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 20 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 228 PHE Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 456 THR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A C 64 GLN 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 = 0.3411 r_free = 0.3411 target = 0.080882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.054903 restraints weight = 247596.052| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 6.42 r_work: 0.2580 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17264 Z= 0.168 Angle : 0.605 15.286 23587 Z= 0.306 Chirality : 0.045 0.217 2689 Planarity : 0.004 0.042 2890 Dihedral : 8.395 71.389 2898 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.91 % Allowed : 9.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.19), residues: 2022 helix: 2.45 (0.21), residues: 578 sheet: 1.25 (0.21), residues: 575 loop : 0.80 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 315 HIS 0.006 0.001 HIS D 267 PHE 0.019 0.002 PHE D 433 TYR 0.023 0.002 TYR B 299 ARG 0.004 0.000 ARG M 459 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 9) link_NAG-ASN : angle 2.16937 ( 27) link_ALPHA1-6 : bond 0.00882 ( 4) link_ALPHA1-6 : angle 1.71353 ( 12) link_BETA1-4 : bond 0.00243 ( 12) link_BETA1-4 : angle 1.68673 ( 36) link_ALPHA1-3 : bond 0.00944 ( 4) link_ALPHA1-3 : angle 1.48595 ( 12) hydrogen bonds : bond 0.04384 ( 837) hydrogen bonds : angle 4.63929 ( 2726) SS BOND : bond 0.00271 ( 8) SS BOND : angle 0.95734 ( 16) covalent geometry : bond 0.00373 (17227) covalent geometry : angle 0.59552 (23484) *********************** 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 271 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 1.943 Fit side-chains revert: symmetry clash REVERT: A 55 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8633 (mmm) REVERT: B 243 ASN cc_start: 0.8108 (t0) cc_final: 0.7745 (t0) REVERT: B 306 PHE cc_start: 0.8653 (t80) cc_final: 0.7291 (t80) REVERT: C 224 GLN cc_start: 0.8900 (tp40) cc_final: 0.8485 (tp40) REVERT: C 243 ASN cc_start: 0.7618 (t0) cc_final: 0.6871 (t0) REVERT: C 261 MET cc_start: 0.9404 (mmm) cc_final: 0.9171 (mmm) REVERT: D 227 MET cc_start: 0.9008 (mmm) cc_final: 0.8582 (mmm) REVERT: E 83 MET cc_start: 0.9231 (mmt) cc_final: 0.8768 (mmt) REVERT: E 104 HIS cc_start: 0.6723 (OUTLIER) cc_final: 0.6182 (t-90) REVERT: E 170 LYS cc_start: 0.8595 (mttt) cc_final: 0.8346 (mtpp) REVERT: E 179 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8480 (mtp) REVERT: E 315 TRP cc_start: 0.8035 (m100) cc_final: 0.7750 (m100) REVERT: K 433 GLU cc_start: 0.7798 (mp0) cc_final: 0.7572 (mp0) REVERT: K 460 ASP cc_start: 0.8093 (t0) cc_final: 0.7798 (t0) REVERT: L 433 GLU cc_start: 0.8680 (tt0) cc_final: 0.8468 (pt0) REVERT: L 460 ASP cc_start: 0.8381 (t0) cc_final: 0.8159 (t0) REVERT: L 472 ASN cc_start: 0.8618 (t0) cc_final: 0.8257 (t0) REVERT: L 474 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8645 (mmmm) REVERT: L 482 TYR cc_start: 0.9121 (m-80) cc_final: 0.8760 (m-80) REVERT: M 459 ARG cc_start: 0.8111 (pmt-80) cc_final: 0.7801 (pmt-80) REVERT: M 460 ASP cc_start: 0.8546 (t0) cc_final: 0.8124 (p0) REVERT: M 469 GLU cc_start: 0.8460 (mp0) cc_final: 0.7811 (mp0) REVERT: M 474 LYS cc_start: 0.8627 (mttp) cc_final: 0.8354 (mttp) outliers start: 33 outliers final: 17 residues processed: 253 average time/residue: 0.3072 time to fit residues: 116.2214 Evaluate side-chains 232 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 145 LEU 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 87 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 Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 43 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.079937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.054264 restraints weight = 240018.235| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 6.27 r_work: 0.2574 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2574 ------------------------------------------------------------------------------- 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 = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17264 Z= 0.151 Angle : 0.584 10.806 23587 Z= 0.295 Chirality : 0.045 0.234 2689 Planarity : 0.003 0.038 2890 Dihedral : 7.790 65.607 2898 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.03 % Allowed : 10.13 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 2022 helix: 2.49 (0.21), residues: 578 sheet: 1.17 (0.20), residues: 623 loop : 0.76 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 237 HIS 0.002 0.001 HIS E 204 PHE 0.017 0.002 PHE A 31 TYR 0.024 0.002 TYR D 220 ARG 0.007 0.000 ARG D 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 9) link_NAG-ASN : angle 2.07878 ( 27) link_ALPHA1-6 : bond 0.00886 ( 4) link_ALPHA1-6 : angle 1.72831 ( 12) link_BETA1-4 : bond 0.00220 ( 12) link_BETA1-4 : angle 1.72635 ( 36) link_ALPHA1-3 : bond 0.00803 ( 4) link_ALPHA1-3 : angle 1.75276 ( 12) hydrogen bonds : bond 0.03811 ( 837) hydrogen bonds : angle 4.44129 ( 2726) SS BOND : bond 0.00251 ( 8) SS BOND : angle 0.82578 ( 16) covalent geometry : bond 0.00338 (17227) covalent geometry : angle 0.57426 (23484) *********************** 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 258 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8776 (mmm) REVERT: A 286 MET cc_start: 0.8370 (mmp) cc_final: 0.7727 (ppp) REVERT: B 243 ASN cc_start: 0.7903 (t0) cc_final: 0.7653 (t0) REVERT: C 30 ASP cc_start: 0.9090 (m-30) cc_final: 0.8781 (t0) REVERT: C 224 GLN cc_start: 0.8929 (tp40) cc_final: 0.8458 (tp40) REVERT: C 243 ASN cc_start: 0.7691 (t0) cc_final: 0.6994 (t0) REVERT: C 261 MET cc_start: 0.9413 (mmm) cc_final: 0.9133 (mmm) REVERT: E 104 HIS cc_start: 0.6648 (OUTLIER) cc_final: 0.6131 (t-90) REVERT: E 170 LYS cc_start: 0.8663 (mttt) cc_final: 0.8415 (mtpp) REVERT: K 433 GLU cc_start: 0.7834 (mp0) cc_final: 0.7589 (mp0) REVERT: K 460 ASP cc_start: 0.8043 (t0) cc_final: 0.7735 (t0) REVERT: L 472 ASN cc_start: 0.8636 (t0) cc_final: 0.8319 (t0) REVERT: L 474 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8669 (mmmm) REVERT: L 482 TYR cc_start: 0.9121 (m-80) cc_final: 0.8808 (m-80) REVERT: M 459 ARG cc_start: 0.8231 (pmt-80) cc_final: 0.7883 (pmt-80) REVERT: M 460 ASP cc_start: 0.8526 (t0) cc_final: 0.8138 (p0) REVERT: M 469 GLU cc_start: 0.8445 (mp0) cc_final: 0.7817 (mp0) REVERT: M 474 LYS cc_start: 0.8513 (mttp) cc_final: 0.8282 (mttp) outliers start: 35 outliers final: 22 residues processed: 245 average time/residue: 0.3421 time to fit residues: 127.2777 Evaluate side-chains 242 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 125 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052779 restraints weight = 218675.954| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 6.03 r_work: 0.2544 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17264 Z= 0.187 Angle : 0.603 14.835 23587 Z= 0.303 Chirality : 0.045 0.235 2689 Planarity : 0.003 0.031 2890 Dihedral : 7.553 61.620 2898 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.03 % Allowed : 10.97 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 2022 helix: 2.42 (0.21), residues: 582 sheet: 1.05 (0.20), residues: 647 loop : 0.69 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 315 HIS 0.003 0.001 HIS C 107 PHE 0.023 0.002 PHE B 307 TYR 0.024 0.002 TYR D 299 ARG 0.006 0.001 ARG D 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 9) link_NAG-ASN : angle 1.97184 ( 27) link_ALPHA1-6 : bond 0.00872 ( 4) link_ALPHA1-6 : angle 1.70446 ( 12) link_BETA1-4 : bond 0.00245 ( 12) link_BETA1-4 : angle 1.79214 ( 36) link_ALPHA1-3 : bond 0.00730 ( 4) link_ALPHA1-3 : angle 1.72239 ( 12) hydrogen bonds : bond 0.03840 ( 837) hydrogen bonds : angle 4.40222 ( 2726) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.04476 ( 16) covalent geometry : bond 0.00422 (17227) covalent geometry : angle 0.59293 (23484) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 2.286 Fit side-chains revert: symmetry clash REVERT: A 55 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8711 (mmm) REVERT: A 286 MET cc_start: 0.8374 (mmp) cc_final: 0.7682 (ppp) REVERT: B 243 ASN cc_start: 0.8012 (t0) cc_final: 0.7764 (t0) REVERT: C 30 ASP cc_start: 0.9078 (m-30) cc_final: 0.8785 (t0) REVERT: C 224 GLN cc_start: 0.8929 (tp40) cc_final: 0.8485 (tp40) REVERT: C 243 ASN cc_start: 0.7720 (t0) cc_final: 0.7032 (t0) REVERT: E 83 MET cc_start: 0.9376 (mmt) cc_final: 0.8716 (mmm) REVERT: E 104 HIS cc_start: 0.6796 (OUTLIER) cc_final: 0.6245 (t-90) REVERT: E 170 LYS cc_start: 0.8665 (mttt) cc_final: 0.8410 (mtpp) REVERT: E 179 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8532 (mtp) REVERT: E 256 MET cc_start: 0.8315 (tpp) cc_final: 0.8038 (tpp) REVERT: E 264 MET cc_start: 0.9306 (ttm) cc_final: 0.9099 (ttm) REVERT: K 433 GLU cc_start: 0.7906 (mp0) cc_final: 0.7656 (mp0) REVERT: K 459 ARG cc_start: 0.8480 (pmt-80) cc_final: 0.8031 (ppt170) REVERT: K 460 ASP cc_start: 0.7986 (t0) cc_final: 0.7682 (t0) REVERT: K 464 ASN cc_start: 0.8698 (m110) cc_final: 0.8460 (m-40) REVERT: L 472 ASN cc_start: 0.8693 (t0) cc_final: 0.8351 (t0) REVERT: L 474 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8718 (mmmm) REVERT: L 482 TYR cc_start: 0.9153 (m-80) cc_final: 0.8768 (m-80) REVERT: M 459 ARG cc_start: 0.8386 (pmt-80) cc_final: 0.8025 (pmt-80) REVERT: M 460 ASP cc_start: 0.8540 (t0) cc_final: 0.8101 (p0) REVERT: M 469 GLU cc_start: 0.8401 (mp0) cc_final: 0.7753 (mp0) REVERT: M 474 LYS cc_start: 0.8439 (mttp) cc_final: 0.8236 (mttp) outliers start: 35 outliers final: 25 residues processed: 247 average time/residue: 0.3194 time to fit residues: 121.7338 Evaluate side-chains 247 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 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 20 LEU Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 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 218 ILE 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 467 TYR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 147 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 74 optimal weight: 0.2980 chunk 98 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.052513 restraints weight = 236158.574| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 6.19 r_work: 0.2536 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.4182 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= 0.170 Angle : 0.594 14.813 23587 Z= 0.296 Chirality : 0.045 0.238 2689 Planarity : 0.003 0.039 2890 Dihedral : 7.252 58.341 2898 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.97 % Allowed : 11.20 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.19), residues: 2022 helix: 2.53 (0.21), residues: 578 sheet: 1.08 (0.21), residues: 647 loop : 0.69 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 315 HIS 0.002 0.001 HIS C 107 PHE 0.033 0.002 PHE K 455 TYR 0.024 0.002 TYR B 299 ARG 0.007 0.000 ARG D 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 9) link_NAG-ASN : angle 1.89921 ( 27) link_ALPHA1-6 : bond 0.00899 ( 4) link_ALPHA1-6 : angle 1.65516 ( 12) link_BETA1-4 : bond 0.00254 ( 12) link_BETA1-4 : angle 1.72254 ( 36) link_ALPHA1-3 : bond 0.00777 ( 4) link_ALPHA1-3 : angle 1.67662 ( 12) hydrogen bonds : bond 0.03658 ( 837) hydrogen bonds : angle 4.33685 ( 2726) SS BOND : bond 0.00166 ( 8) SS BOND : angle 0.82992 ( 16) covalent geometry : bond 0.00386 (17227) covalent geometry : angle 0.58509 (23484) *********************** 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 262 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 MET cc_start: 0.8374 (mmp) cc_final: 0.7461 (mtt) REVERT: B 243 ASN cc_start: 0.8049 (t0) cc_final: 0.7810 (t0) REVERT: C 30 ASP cc_start: 0.9079 (m-30) cc_final: 0.8788 (t0) REVERT: C 224 GLN cc_start: 0.8947 (tp40) cc_final: 0.8485 (tp40) REVERT: C 243 ASN cc_start: 0.7762 (t0) cc_final: 0.7057 (t0) REVERT: D 221 PHE cc_start: 0.8885 (m-80) cc_final: 0.8651 (m-80) REVERT: D 437 LEU cc_start: 0.8643 (tt) cc_final: 0.8190 (mp) REVERT: E 104 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6266 (t-90) REVERT: E 170 LYS cc_start: 0.8723 (mttt) cc_final: 0.8469 (mtpp) REVERT: E 179 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8491 (mtp) REVERT: E 294 MET cc_start: 0.8111 (ttp) cc_final: 0.7897 (ttp) REVERT: K 3 GLN cc_start: 0.8439 (mp10) cc_final: 0.8129 (mp10) REVERT: K 6 GLU cc_start: 0.8596 (pm20) cc_final: 0.8326 (pm20) REVERT: K 433 GLU cc_start: 0.7941 (mp0) cc_final: 0.7652 (mp0) REVERT: K 459 ARG cc_start: 0.8533 (pmt-80) cc_final: 0.7959 (ppt170) REVERT: K 460 ASP cc_start: 0.8068 (t0) cc_final: 0.7744 (t0) REVERT: K 464 ASN cc_start: 0.8733 (m110) cc_final: 0.8510 (m-40) REVERT: K 468 LEU cc_start: 0.8827 (tp) cc_final: 0.8510 (tp) REVERT: K 470 MET cc_start: 0.8343 (mtm) cc_final: 0.7894 (mpp) REVERT: K 474 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7949 (mmtt) REVERT: L 463 LYS cc_start: 0.9213 (mtmm) cc_final: 0.8943 (pttm) REVERT: L 472 ASN cc_start: 0.8700 (t0) cc_final: 0.8008 (t0) REVERT: L 474 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8714 (mtmm) REVERT: L 482 TYR cc_start: 0.9150 (m-80) cc_final: 0.8703 (m-80) REVERT: M 459 ARG cc_start: 0.8428 (pmt-80) cc_final: 0.8020 (pmt-80) REVERT: M 469 GLU cc_start: 0.8401 (mp0) cc_final: 0.7738 (mp0) REVERT: M 474 LYS cc_start: 0.8417 (mttp) cc_final: 0.8210 (mttp) outliers start: 33 outliers final: 26 residues processed: 246 average time/residue: 0.2738 time to fit residues: 102.3316 Evaluate side-chains 247 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 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 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 179 MET Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 VAL Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 467 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 103 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 171 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 142 optimal weight: 0.0170 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.053674 restraints weight = 265584.676| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 6.46 r_work: 0.2557 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17264 Z= 0.115 Angle : 0.573 14.247 23587 Z= 0.282 Chirality : 0.044 0.241 2689 Planarity : 0.003 0.035 2890 Dihedral : 6.712 56.247 2898 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.91 % Allowed : 11.31 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2022 helix: 2.50 (0.21), residues: 578 sheet: 1.25 (0.21), residues: 599 loop : 0.64 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 315 HIS 0.002 0.000 HIS E 240 PHE 0.017 0.001 PHE C 433 TYR 0.025 0.001 TYR D 220 ARG 0.007 0.000 ARG D 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 9) link_NAG-ASN : angle 1.74024 ( 27) link_ALPHA1-6 : bond 0.01038 ( 4) link_ALPHA1-6 : angle 1.58191 ( 12) link_BETA1-4 : bond 0.00290 ( 12) link_BETA1-4 : angle 1.51975 ( 36) link_ALPHA1-3 : bond 0.00923 ( 4) link_ALPHA1-3 : angle 1.53414 ( 12) hydrogen bonds : bond 0.03436 ( 837) hydrogen bonds : angle 4.18208 ( 2726) SS BOND : bond 0.00147 ( 8) SS BOND : angle 0.76874 ( 16) covalent geometry : bond 0.00252 (17227) covalent geometry : angle 0.56592 (23484) *********************** 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 267 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 MET cc_start: 0.8316 (mmp) cc_final: 0.7656 (ppp) REVERT: B 243 ASN cc_start: 0.8049 (t0) cc_final: 0.7834 (t0) REVERT: C 30 ASP cc_start: 0.9062 (m-30) cc_final: 0.8785 (t0) REVERT: C 224 GLN cc_start: 0.8920 (tp40) cc_final: 0.8678 (tp40) REVERT: C 243 ASN cc_start: 0.7747 (t0) cc_final: 0.7034 (t0) REVERT: D 270 GLU cc_start: 0.8710 (pt0) cc_final: 0.8486 (pp20) REVERT: D 437 LEU cc_start: 0.8624 (tt) cc_final: 0.8181 (mp) REVERT: E 83 MET cc_start: 0.9423 (mmt) cc_final: 0.9169 (mmt) REVERT: E 104 HIS cc_start: 0.6780 (OUTLIER) cc_final: 0.6227 (t70) REVERT: E 170 LYS cc_start: 0.8721 (mttt) cc_final: 0.8466 (mtpp) REVERT: E 179 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8501 (mtp) REVERT: E 260 LEU cc_start: 0.9098 (pp) cc_final: 0.8821 (mp) REVERT: K 3 GLN cc_start: 0.8528 (mp10) cc_final: 0.8207 (mp10) REVERT: K 433 GLU cc_start: 0.7990 (mp0) cc_final: 0.7706 (mp0) REVERT: K 459 ARG cc_start: 0.8530 (pmt-80) cc_final: 0.8019 (ppt170) REVERT: K 460 ASP cc_start: 0.8082 (t0) cc_final: 0.7752 (t0) REVERT: K 464 ASN cc_start: 0.8710 (m110) cc_final: 0.8488 (m-40) REVERT: K 468 LEU cc_start: 0.8571 (tp) cc_final: 0.8247 (tp) REVERT: K 469 GLU cc_start: 0.8254 (mp0) cc_final: 0.7995 (mp0) REVERT: K 470 MET cc_start: 0.8450 (mtm) cc_final: 0.7896 (mpp) REVERT: K 474 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8053 (mmtt) REVERT: L 463 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8946 (pttm) REVERT: L 472 ASN cc_start: 0.8779 (t0) cc_final: 0.8539 (t0) REVERT: L 474 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8719 (mmmm) REVERT: L 482 TYR cc_start: 0.9157 (m-80) cc_final: 0.8716 (m-80) REVERT: M 459 ARG cc_start: 0.8524 (pmt-80) cc_final: 0.8049 (pmt-80) REVERT: M 460 ASP cc_start: 0.8554 (t70) cc_final: 0.8017 (p0) REVERT: M 469 GLU cc_start: 0.8396 (mp0) cc_final: 0.7723 (mp0) outliers start: 32 outliers final: 24 residues processed: 252 average time/residue: 0.3198 time to fit residues: 121.5609 Evaluate side-chains 248 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 66 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.077881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.052294 restraints weight = 248499.367| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 6.26 r_work: 0.2524 rms_B_bonded: 5.46 restraints_weight: 2.0000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17264 Z= 0.196 Angle : 0.613 13.816 23587 Z= 0.303 Chirality : 0.045 0.251 2689 Planarity : 0.003 0.027 2890 Dihedral : 6.829 55.252 2897 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.69 % Allowed : 11.59 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 2022 helix: 2.52 (0.21), residues: 578 sheet: 1.22 (0.21), residues: 599 loop : 0.55 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 315 HIS 0.002 0.001 HIS C 107 PHE 0.016 0.002 PHE C 433 TYR 0.028 0.002 TYR D 220 ARG 0.005 0.000 ARG D 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 9) link_NAG-ASN : angle 1.85473 ( 27) link_ALPHA1-6 : bond 0.00848 ( 4) link_ALPHA1-6 : angle 1.57038 ( 12) link_BETA1-4 : bond 0.00283 ( 12) link_BETA1-4 : angle 1.74922 ( 36) link_ALPHA1-3 : bond 0.00731 ( 4) link_ALPHA1-3 : angle 1.77659 ( 12) hydrogen bonds : bond 0.03631 ( 837) hydrogen bonds : angle 4.33537 ( 2726) SS BOND : bond 0.00154 ( 8) SS BOND : angle 0.99921 ( 16) covalent geometry : bond 0.00446 (17227) covalent geometry : angle 0.60388 (23484) *********************** 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 254 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 243 ASN cc_start: 0.8094 (t0) cc_final: 0.7888 (t0) REVERT: C 30 ASP cc_start: 0.9071 (m-30) cc_final: 0.8794 (t0) REVERT: C 224 GLN cc_start: 0.8926 (tp40) cc_final: 0.8667 (tp40) REVERT: C 243 ASN cc_start: 0.7822 (t0) cc_final: 0.7114 (t0) REVERT: D 270 GLU cc_start: 0.8710 (pt0) cc_final: 0.8490 (pp20) REVERT: E 170 LYS cc_start: 0.8735 (mttt) cc_final: 0.8483 (mtpp) REVERT: E 179 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8550 (mtp) REVERT: K 433 GLU cc_start: 0.8013 (mp0) cc_final: 0.7718 (mp0) REVERT: K 459 ARG cc_start: 0.8598 (pmt-80) cc_final: 0.8121 (ppt170) REVERT: K 460 ASP cc_start: 0.8163 (t0) cc_final: 0.7849 (t0) REVERT: K 469 GLU cc_start: 0.8264 (mp0) cc_final: 0.7996 (mp0) REVERT: K 470 MET cc_start: 0.8464 (mtm) cc_final: 0.7760 (mpp) REVERT: K 474 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8091 (mmtt) REVERT: L 472 ASN cc_start: 0.8751 (t0) cc_final: 0.8448 (t0) REVERT: L 474 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8656 (mmmm) REVERT: L 482 TYR cc_start: 0.9176 (m-80) cc_final: 0.8696 (m-80) REVERT: M 3 GLN cc_start: 0.8391 (mp10) cc_final: 0.8130 (mp10) REVERT: M 459 ARG cc_start: 0.8615 (pmt-80) cc_final: 0.8186 (pmt-80) REVERT: M 469 GLU cc_start: 0.8337 (mp0) cc_final: 0.7629 (mp0) REVERT: M 470 MET cc_start: 0.8800 (mtp) cc_final: 0.8535 (mtp) outliers start: 28 outliers final: 27 residues processed: 240 average time/residue: 0.2851 time to fit residues: 104.3445 Evaluate side-chains 250 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 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 132 THR Chi-restraints excluded: chain D residue 165 GLU 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 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 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 L residue 497 THR Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 33 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: C 64 GLN D 224 GLN ** L 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.077398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.051730 restraints weight = 258726.223| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 6.34 r_work: 0.2505 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 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 = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17264 Z= 0.205 Angle : 0.623 13.840 23587 Z= 0.309 Chirality : 0.045 0.252 2689 Planarity : 0.003 0.032 2890 Dihedral : 6.886 55.140 2897 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.14 % Allowed : 11.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2022 helix: 2.51 (0.21), residues: 573 sheet: 1.19 (0.21), residues: 587 loop : 0.48 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 315 HIS 0.003 0.001 HIS C 107 PHE 0.016 0.002 PHE C 433 TYR 0.026 0.002 TYR B 299 ARG 0.008 0.000 ARG D 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 9) link_NAG-ASN : angle 1.82569 ( 27) link_ALPHA1-6 : bond 0.00859 ( 4) link_ALPHA1-6 : angle 1.57324 ( 12) link_BETA1-4 : bond 0.00275 ( 12) link_BETA1-4 : angle 1.77944 ( 36) link_ALPHA1-3 : bond 0.00736 ( 4) link_ALPHA1-3 : angle 1.70058 ( 12) hydrogen bonds : bond 0.03688 ( 837) hydrogen bonds : angle 4.38052 ( 2726) SS BOND : bond 0.00145 ( 8) SS BOND : angle 1.03905 ( 16) covalent geometry : bond 0.00466 (17227) covalent geometry : angle 0.61493 (23484) *********************** 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 261 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 243 ASN cc_start: 0.8114 (t0) cc_final: 0.7910 (t0) REVERT: C 30 ASP cc_start: 0.9090 (m-30) cc_final: 0.8814 (t0) REVERT: C 224 GLN cc_start: 0.8938 (tp40) cc_final: 0.7684 (tp40) REVERT: C 243 ASN cc_start: 0.7852 (t0) cc_final: 0.7151 (t0) REVERT: D 270 GLU cc_start: 0.8711 (pt0) cc_final: 0.8492 (pp20) REVERT: D 437 LEU cc_start: 0.8642 (tt) cc_final: 0.8197 (mp) REVERT: E 83 MET cc_start: 0.9358 (mmt) cc_final: 0.9076 (mmt) REVERT: E 104 HIS cc_start: 0.6862 (OUTLIER) cc_final: 0.6264 (t70) REVERT: E 170 LYS cc_start: 0.8773 (mttt) cc_final: 0.8512 (mtpp) REVERT: E 179 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8550 (mtp) REVERT: K 3 GLN cc_start: 0.8588 (mp10) cc_final: 0.8306 (mp10) REVERT: K 433 GLU cc_start: 0.7987 (mp0) cc_final: 0.7718 (mp0) REVERT: K 459 ARG cc_start: 0.8647 (pmt-80) cc_final: 0.8205 (ppt170) REVERT: K 460 ASP cc_start: 0.8209 (t0) cc_final: 0.7917 (t0) REVERT: K 470 MET cc_start: 0.8509 (mtm) cc_final: 0.7723 (mpp) REVERT: K 472 ASN cc_start: 0.8453 (m110) cc_final: 0.7240 (t0) REVERT: K 474 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7595 (mmtp) REVERT: L 472 ASN cc_start: 0.8735 (t0) cc_final: 0.8438 (t0) REVERT: L 474 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8683 (mmmm) REVERT: L 482 TYR cc_start: 0.9164 (m-80) cc_final: 0.8639 (m-80) REVERT: M 3 GLN cc_start: 0.8419 (mp10) cc_final: 0.8152 (mp10) REVERT: M 459 ARG cc_start: 0.8636 (pmt-80) cc_final: 0.8245 (pmt-80) REVERT: M 460 ASP cc_start: 0.8552 (t0) cc_final: 0.8049 (p0) outliers start: 36 outliers final: 31 residues processed: 244 average time/residue: 0.2973 time to fit residues: 110.1236 Evaluate side-chains 254 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 B residue 305 ILE Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 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 132 THR Chi-restraints excluded: chain D residue 165 GLU 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 179 MET Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 467 TYR Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 497 THR Chi-restraints excluded: chain L residue 467 TYR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 VAL Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain M residue 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 135 optimal weight: 0.0040 chunk 145 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 68 optimal weight: 0.1980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.051831 restraints weight = 258872.466| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 6.36 r_work: 0.2510 rms_B_bonded: 5.50 restraints_weight: 2.0000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.2514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.199 17264 Z= 0.267 Angle : 0.879 59.200 23587 Z= 0.490 Chirality : 0.045 0.489 2689 Planarity : 0.005 0.153 2890 Dihedral : 6.884 55.168 2897 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.97 % Allowed : 11.76 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2022 helix: 2.51 (0.21), residues: 573 sheet: 1.19 (0.21), residues: 587 loop : 0.48 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 315 HIS 0.003 0.001 HIS C 107 PHE 0.042 0.002 PHE M 455 TYR 0.026 0.002 TYR B 299 ARG 0.057 0.001 ARG D 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 9) link_NAG-ASN : angle 1.83842 ( 27) link_ALPHA1-6 : bond 0.00907 ( 4) link_ALPHA1-6 : angle 1.61296 ( 12) link_BETA1-4 : bond 0.00271 ( 12) link_BETA1-4 : angle 1.77190 ( 36) link_ALPHA1-3 : bond 0.00772 ( 4) link_ALPHA1-3 : angle 1.75350 ( 12) hydrogen bonds : bond 0.03674 ( 837) hydrogen bonds : angle 4.39390 ( 2726) SS BOND : bond 0.00131 ( 8) SS BOND : angle 1.01213 ( 16) covalent geometry : bond 0.00562 (17227) covalent geometry : angle 0.87346 (23484) ********************** 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: 33 poor density : 221 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 MET cc_start: 0.8375 (mmp) cc_final: 0.7455 (mtt) REVERT: B 243 ASN cc_start: 0.8108 (t0) cc_final: 0.7907 (t0) REVERT: C 30 ASP cc_start: 0.9099 (m-30) cc_final: 0.8823 (t0) REVERT: C 243 ASN cc_start: 0.7850 (t0) cc_final: 0.7148 (t0) REVERT: D 270 GLU cc_start: 0.8716 (pt0) cc_final: 0.8492 (pp20) REVERT: D 437 LEU cc_start: 0.8641 (tt) cc_final: 0.8196 (mp) REVERT: E 83 MET cc_start: 0.9362 (mmt) cc_final: 0.9075 (mmt) REVERT: E 104 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6244 (t70) REVERT: E 170 LYS cc_start: 0.8771 (mttt) cc_final: 0.8513 (mtpp) REVERT: E 179 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8542 (mtp) REVERT: K 3 GLN cc_start: 0.8579 (mp10) cc_final: 0.8284 (mp10) REVERT: K 433 GLU cc_start: 0.7971 (mp0) cc_final: 0.7660 (mp0) REVERT: K 459 ARG cc_start: 0.8643 (pmt-80) cc_final: 0.8202 (ppt170) REVERT: K 460 ASP cc_start: 0.8221 (t0) cc_final: 0.7908 (t0) REVERT: K 470 MET cc_start: 0.8510 (mtm) cc_final: 0.7733 (mpp) REVERT: K 472 ASN cc_start: 0.8456 (m110) cc_final: 0.7237 (t0) REVERT: K 474 LYS cc_start: 0.8429 (mmtt) cc_final: 0.7575 (mmtp) REVERT: L 472 ASN cc_start: 0.8740 (t0) cc_final: 0.8439 (t0) REVERT: L 474 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8678 (mmmm) REVERT: L 482 TYR cc_start: 0.9163 (m-80) cc_final: 0.8640 (m-80) REVERT: M 3 GLN cc_start: 0.8418 (mp10) cc_final: 0.8143 (mp10) REVERT: M 459 ARG cc_start: 0.8632 (pmt-80) cc_final: 0.8244 (pmt-80) REVERT: M 460 ASP cc_start: 0.8550 (t0) cc_final: 0.8046 (p0) outliers start: 33 outliers final: 28 residues processed: 238 average time/residue: 0.3518 time to fit residues: 126.8593 Evaluate side-chains 250 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 B residue 305 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 218 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 40 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE 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 179 MET Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 441 SER 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 L residue 497 THR Chi-restraints excluded: chain M residue 467 TYR Chi-restraints excluded: chain M residue 480 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN ** L 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.051973 restraints weight = 227035.908| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 6.05 r_work: 0.2521 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.2526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.199 17264 Z= 0.267 Angle : 0.879 59.200 23587 Z= 0.490 Chirality : 0.045 0.489 2689 Planarity : 0.005 0.153 2890 Dihedral : 6.884 55.168 2897 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.80 % Allowed : 11.87 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2022 helix: 2.51 (0.21), residues: 573 sheet: 1.19 (0.21), residues: 587 loop : 0.48 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 315 HIS 0.003 0.001 HIS C 107 PHE 0.042 0.002 PHE M 455 TYR 0.026 0.002 TYR B 299 ARG 0.057 0.001 ARG D 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 9) link_NAG-ASN : angle 1.83842 ( 27) link_ALPHA1-6 : bond 0.00907 ( 4) link_ALPHA1-6 : angle 1.61296 ( 12) link_BETA1-4 : bond 0.00271 ( 12) link_BETA1-4 : angle 1.77190 ( 36) link_ALPHA1-3 : bond 0.00772 ( 4) link_ALPHA1-3 : angle 1.75350 ( 12) hydrogen bonds : bond 0.03674 ( 837) hydrogen bonds : angle 4.39390 ( 2726) SS BOND : bond 0.00131 ( 8) SS BOND : angle 1.01213 ( 16) covalent geometry : bond 0.00562 (17227) covalent geometry : angle 0.87347 (23484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11369.90 seconds wall clock time: 202 minutes 10.34 seconds (12130.34 seconds total)