Starting phenix.real_space_refine on Fri Jun 5 22:17:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x5y_66601/06_2026/9x5y_66601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x5y_66601/06_2026/9x5y_66601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x5y_66601/06_2026/9x5y_66601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x5y_66601/06_2026/9x5y_66601.map" model { file = "/net/cci-nas-00/data/ceres_data/9x5y_66601/06_2026/9x5y_66601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x5y_66601/06_2026/9x5y_66601.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10056 atoms to isotropic. 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 66 5.16 5 C 9954 2.51 5 N 2715 2.21 5 O 3195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15930 Number of models: 1 Model: "" Number of chains: 27 Chain: "G" Number of atoms: 2570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} Conformer: "B" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} bond proxies already assigned to first conformer: 2587 Chain: "I" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 1 Chain: "J" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 904 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 2570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} Conformer: "B" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} bond proxies already assigned to first conformer: 2587 Chain: "B" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 1 Chain: "C" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 904 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 2570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} Conformer: "B" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} bond proxies already assigned to first conformer: 2587 Chain: "F" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 1 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 904 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" 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: "O" 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: "P" 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: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" 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: "S" 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: "T" 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: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" 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: "W" 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: "X" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ASER G 39 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER G 39 " occ=0.50 residue: pdb=" N AASN G 43 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN G 43 " occ=0.50 residue: pdb=" N ASER G 306 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER G 306 " occ=0.50 residue: pdb=" N ASER A 39 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 39 " occ=0.50 residue: pdb=" N AASN A 43 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 43 " occ=0.50 residue: pdb=" N ASER A 306 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 306 " occ=0.50 residue: pdb=" N ASER E 39 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 39 " occ=0.50 residue: pdb=" N AASN E 43 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN E 43 " occ=0.50 residue: pdb=" N ASER E 306 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 306 " occ=0.50 Time building chain proxies: 5.18, per 1000 atoms: 0.33 Number of scatterers: 15930 At special positions: 0 Unit cell: (141.93, 139.44, 140.27, 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 66 16.00 O 3195 8.00 N 2715 7.00 C 9954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 57 " distance=2.04 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 72 " distance=2.03 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 143 " distance=2.03 Simple disulfide: pdb=" SG CYS G 181 " - pdb=" SG CYS G 275 " distance=2.00 Simple disulfide: pdb=" SG CYS G 295 " - pdb=" SG CYS G 321 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 104 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 181 " - pdb=" SG CYS A 275 " distance=2.01 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 104 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 104 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 57 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS E 181 " - pdb=" SG CYS E 275 " distance=2.00 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 321 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 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=1, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 4 " - " MAN Q 5 " " BMA U 3 " - " MAN U 6 " " MAN U 4 " - " MAN U 5 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 401 " - " ASN A 233 " " NAG A 402 " - " ASN A 25 " " NAG A 403 " - " ASN A 59 " " NAG E 401 " - " ASN E 233 " " NAG E 402 " - " ASN E 25 " " NAG E 403 " - " ASN E 59 " " NAG G 401 " - " ASN G 233 " " NAG G 402 " - " ASN G 25 " " NAG G 403 " - " ASN G 59 " " NAG M 1 " - " ASN G 145 " " NAG N 1 " - " ASN G 197 " " NAG O 1 " - " ASN G 304 " " NAG P 1 " - " ASN G 333 " " NAG Q 1 " - " ASN A 145 " " NAG R 1 " - " ASN A 197 " " NAG S 1 " - " ASN A 304 " " NAG T 1 " - " ASN A 333 " " NAG U 1 " - " ASN E 145 " " NAG V 1 " - " ASN E 197 " " NAG W 1 " - " ASN E 304 " " NAG X 1 " - " ASN E 333 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3618 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 45 sheets defined 17.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'G' and resid 61 through 68 Processing helix chain 'G' and resid 98 through 102 removed outlier: 3.506A pdb=" N ARG G 101 " --> pdb=" O MET G 98 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR G 102 " --> pdb=" O HIS G 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 98 through 102' Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'G' and resid 106 through 112 Processing helix chain 'G' and resid 197 through 206 Processing helix chain 'I' and resid 387 through 404 Processing helix chain 'I' and resid 421 through 472 removed outlier: 4.844A pdb=" N ASP I 459 " --> pdb=" O ILE I 455 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU I 460 " --> pdb=" O ASN I 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 37 removed outlier: 3.670A pdb=" N PHE J 37 " --> pdb=" O PHE J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 37 No H-bonds generated for 'chain 'K' and resid 30 through 37' Processing helix chain 'K' and resid 95 through 99 removed outlier: 4.036A pdb=" N ILE K 99 " --> pdb=" O PRO K 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.942A pdb=" N THR A 102 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'B' and resid 387 through 403 removed outlier: 3.652A pdb=" N ALA B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 472 removed outlier: 3.638A pdb=" N LEU B 425 " --> pdb=" O HIS B 421 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 37 removed outlier: 3.720A pdb=" N PHE C 37 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 removed outlier: 4.036A pdb=" N THR C 99 " --> pdb=" O PRO C 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 37 No H-bonds generated for 'chain 'D' and resid 30 through 37' Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.745A pdb=" N ILE D 99 " --> pdb=" O PRO D 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.522A pdb=" N ARG E 101 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 102 " --> pdb=" O HIS E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 102' Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 197 through 206 Processing helix chain 'F' and resid 387 through 404 Processing helix chain 'F' and resid 421 through 473 removed outlier: 3.598A pdb=" N LEU F 425 " --> pdb=" O HIS F 421 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP F 459 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU F 460 " --> pdb=" O ASN F 456 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET F 472 " --> pdb=" O LYS F 468 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU F 473 " --> pdb=" O LEU F 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.705A pdb=" N PHE H 37 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 37 No H-bonds generated for 'chain 'L' and resid 30 through 37' Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.773A pdb=" N ILE L 99 " --> pdb=" O PRO L 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'G' and resid 29 through 31 Processing sheet with id=AA3, first strand: chain 'G' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'G' and resid 43 through 44 removed outlier: 6.076A pdb=" N AASN G 43 " --> pdb=" O ALA G 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 49 through 50 Processing sheet with id=AA6, first strand: chain 'G' and resid 116 through 119 removed outlier: 7.477A pdb=" N VAL G 190 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE G 267 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP G 158 " --> pdb=" O GLY G 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 116 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 173 through 177 Processing sheet with id=AA9, first strand: chain 'G' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.669A pdb=" N MET J 39 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL J 55 " --> pdb=" O MET J 39 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP J 41 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 12 through 13 Processing sheet with id=AB4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AB6, first strand: chain 'K' and resid 66 through 67 removed outlier: 6.391A pdb=" N TRP K 41 " --> pdb=" O LEU K 53 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR K 55 " --> pdb=" O LEU K 39 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU K 39 " --> pdb=" O TYR K 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AB8, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AB9, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AC1, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.072A pdb=" N AASN A 43 " --> pdb=" O ALA A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AC3, first strand: chain 'A' and resid 116 through 119 removed outlier: 7.462A pdb=" N VAL A 190 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A 267 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP A 158 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AC5, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AC6, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AC7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.645A pdb=" N MET C 39 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL C 55 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP C 41 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AD1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AD3, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.377A pdb=" N TRP D 41 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR D 55 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU D 39 " --> pdb=" O TYR D 55 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AD5, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AD6, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AD7, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.066A pdb=" N AASN E 43 " --> pdb=" O ALA E 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AD9, first strand: chain 'E' and resid 116 through 119 removed outlier: 7.482A pdb=" N VAL E 190 " --> pdb=" O PRO E 270 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE E 267 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TRP E 158 " --> pdb=" O GLY E 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 116 through 119 Processing sheet with id=AE2, first strand: chain 'E' and resid 173 through 177 Processing sheet with id=AE3, first strand: chain 'E' and resid 301 through 303 Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.629A pdb=" N MET H 39 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AE7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AE9, first strand: chain 'L' and resid 66 through 67 removed outlier: 6.373A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.23: 1812 1.23 - 1.38: 4302 1.38 - 1.53: 9151 1.53 - 1.68: 908 1.68 - 1.82: 90 Bond restraints: 16263 Sorted by residual: bond pdb=" C ARG G 118 " pdb=" O ARG G 118 " ideal model delta sigma weight residual 1.234 1.088 0.146 1.22e-02 6.72e+03 1.44e+02 bond pdb=" C ARG A 118 " pdb=" O ARG A 118 " ideal model delta sigma weight residual 1.234 1.113 0.121 1.22e-02 6.72e+03 9.79e+01 bond pdb=" C ILE G 117 " pdb=" O ILE G 117 " ideal model delta sigma weight residual 1.236 1.137 0.099 1.00e-02 1.00e+04 9.75e+01 bond pdb=" C LEU I 410 " pdb=" O LEU I 410 " ideal model delta sigma weight residual 1.236 1.122 0.114 1.17e-02 7.31e+03 9.53e+01 bond pdb=" C ARG I 412 " pdb=" O ARG I 412 " ideal model delta sigma weight residual 1.234 1.142 0.092 1.33e-02 5.65e+03 4.82e+01 ... (remaining 16258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 21030 2.12 - 4.23: 874 4.23 - 6.35: 126 6.35 - 8.47: 38 8.47 - 10.58: 9 Bond angle restraints: 22077 Sorted by residual: angle pdb=" CA LEU I 410 " pdb=" C LEU I 410 " pdb=" O LEU I 410 " ideal model delta sigma weight residual 120.46 115.37 5.09 1.07e+00 8.73e-01 2.27e+01 angle pdb=" CA CYS E 181 " pdb=" CB CYS E 181 " pdb=" SG CYS E 181 " ideal model delta sigma weight residual 114.40 103.90 10.50 2.30e+00 1.89e-01 2.08e+01 angle pdb=" CG ARG E 88 " pdb=" CD ARG E 88 " pdb=" NE ARG E 88 " ideal model delta sigma weight residual 112.00 102.83 9.17 2.20e+00 2.07e-01 1.74e+01 angle pdb=" CA CYS G 181 " pdb=" CB CYS G 181 " pdb=" SG CYS G 181 " ideal model delta sigma weight residual 114.40 104.91 9.49 2.30e+00 1.89e-01 1.70e+01 angle pdb=" CA CYS A 181 " pdb=" CB CYS A 181 " pdb=" SG CYS A 181 " ideal model delta sigma weight residual 114.40 104.91 9.49 2.30e+00 1.89e-01 1.70e+01 ... (remaining 22072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 9600 21.41 - 42.82: 532 42.82 - 64.23: 140 64.23 - 85.64: 49 85.64 - 107.05: 20 Dihedral angle restraints: 10341 sinusoidal: 4665 harmonic: 5676 Sorted by residual: dihedral pdb=" CA LEU I 420 " pdb=" C LEU I 420 " pdb=" N HIS I 421 " pdb=" CA HIS I 421 " ideal model delta harmonic sigma weight residual 180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA LEU F 420 " pdb=" C LEU F 420 " pdb=" N HIS F 421 " pdb=" CA HIS F 421 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LEU B 420 " pdb=" C LEU B 420 " pdb=" N HIS B 421 " pdb=" CA HIS B 421 " ideal model delta harmonic sigma weight residual -180.00 -155.21 -24.79 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 10338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1935 0.065 - 0.130: 558 0.130 - 0.195: 83 0.195 - 0.260: 15 0.260 - 0.325: 10 Chirality restraints: 2601 Sorted by residual: chirality pdb=" CB ILE I 454 " pdb=" CA ILE I 454 " pdb=" CG1 ILE I 454 " pdb=" CG2 ILE I 454 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB ILE A 180 " pdb=" CA ILE A 180 " pdb=" CG1 ILE A 180 " pdb=" CG2 ILE A 180 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB VAL A 273 " pdb=" CA VAL A 273 " pdb=" CG1 VAL A 273 " pdb=" CG2 VAL A 273 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 2598 not shown) Planarity restraints: 2808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 70 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C PRO E 70 " -0.059 2.00e-02 2.50e+03 pdb=" O PRO E 70 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS E 71 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 95 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C ARG C 95 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG C 95 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO C 96 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG G 88 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO G 89 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 89 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 89 " 0.037 5.00e-02 4.00e+02 ... (remaining 2805 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 6 2.04 - 2.76: 2426 2.76 - 3.47: 19638 3.47 - 4.19: 39723 4.19 - 4.90: 69905 Nonbonded interactions: 131698 Sorted by model distance: nonbonded pdb=" O LYS F 408 " pdb=" NH2 ARG F 435 " model vdw 1.328 3.120 nonbonded pdb=" OG1 THR I 438 " pdb=" NH1 ARG B 435 " model vdw 1.681 3.120 nonbonded pdb=" NH1 ARG I 435 " pdb=" OG1 THR F 438 " model vdw 1.732 3.120 nonbonded pdb=" NE1 TRP F 368 " pdb=" C SER F 387 " model vdw 1.872 2.680 nonbonded pdb=" OG1 THR A 8 " pdb=" NE1 TRP B 368 " model vdw 1.901 3.120 ... (remaining 131693 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 38 or resid 40 through 42 or resid 44 through 30 \ 5 or resid 307 through 403)) selection = (chain 'E' and (resid 5 through 38 or resid 40 through 42 or resid 44 through 30 \ 5 or resid 307 through 403)) selection = (chain 'G' and (resid 5 through 38 or resid 40 through 42 or resid 44 through 30 \ 5 or resid 307 through 403)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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=1.00 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.240 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.011 0.276 16330 Z= 0.551 Angle : 1.024 10.584 22254 Z= 0.529 Chirality : 0.063 0.325 2601 Planarity : 0.008 0.066 2787 Dihedral : 15.614 107.052 6660 Min Nonbonded Distance : 1.328 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.90 % Allowed : 9.75 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.16), residues: 1992 helix: -1.09 (0.27), residues: 282 sheet: -0.97 (0.20), residues: 615 loop : -1.66 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 101 TYR 0.027 0.003 TYR L 38 PHE 0.035 0.004 PHE K 107 TRP 0.014 0.003 TRP B 368 HIS 0.007 0.002 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.01109 / 0.51 (16263) covalent geometry : angle 0.99422 / 0.52 (22077) SS BOND : bond 0.01162 / 0.53 ( 21) SS BOND : angle 1.75994 / 1.07 ( 42) hydrogen bonds : bond 0.12333 / 8.44 ( 600) hydrogen bonds : angle 7.46015 / 5.15 ( 1686) Misc. bond : bond 0.27640 / 14.55 ( 1) link_ALPHA1-3 : bond 0.00228 / 0.13 ( 6) link_ALPHA1-3 : angle 2.56105 / 1.39 ( 18) link_ALPHA1-6 : bond 0.00518 / 0.24 ( 3) link_ALPHA1-6 : angle 2.07761 / 1.10 ( 9) link_BETA1-4 : bond 0.00982 / 0.67 ( 15) link_BETA1-4 : angle 3.49668 / 2.18 ( 45) link_NAG-ASN : bond 0.00631 / 0.39 ( 21) link_NAG-ASN : angle 3.25405 / 2.01 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 221 time to evaluate : 0.604 Fit side-chains REVERT: G 17 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7857 (ttmm) REVERT: G 88 ARG cc_start: 0.7925 (mpp-170) cc_final: 0.7541 (ptt180) REVERT: I 423 GLU cc_start: 0.8032 (mp0) cc_final: 0.7806 (mp0) REVERT: J 106 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: K 28 ARG cc_start: 0.7436 (ttp-170) cc_final: 0.7187 (mtp180) REVERT: K 126 ILE cc_start: 0.6548 (OUTLIER) cc_final: 0.6221 (pp) REVERT: A 75 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7899 (tttp) REVERT: A 88 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7623 (ttt-90) REVERT: B 397 LYS cc_start: 0.8673 (mttp) cc_final: 0.8463 (mttp) REVERT: B 465 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7837 (tp) REVERT: C 86 SER cc_start: 0.8136 (m) cc_final: 0.7614 (p) REVERT: C 91 MET cc_start: 0.7391 (mtm) cc_final: 0.7145 (mtp) REVERT: D 27 GLN cc_start: 0.7052 (mm-40) cc_final: 0.6768 (mm-40) REVERT: E 38 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8151 (tmtt) REVERT: F 392 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7965 (mp) REVERT: H 86 SER cc_start: 0.8064 (m) cc_final: 0.7483 (p) REVERT: H 106 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7543 (tm-30) outliers start: 66 outliers final: 33 residues processed: 282 average time/residue: 0.5839 time to fit residues: 182.5351 Evaluate side-chains 205 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 116 HIS G 148 ASN G 171 ASN G 218 ASN G 264 GLN I 393 ASN I 400 ASN I 421 HIS I 442 GLN I 456 ASN J 82 ASN J 120 GLN K 37 ASN K 44 GLN K 48 GLN A 116 HIS A 171 ASN A 218 ASN A 264 GLN B 393 ASN B 398 ASN B 421 HIS C 3 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN E 116 HIS E 148 ASN E 171 ASN F 400 ASN F 421 HIS F 442 GLN H 14 GLN H 106 GLN L 44 GLN L 48 GLN L 66 ASN L 120 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.179440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112006 restraints weight = 78364.717| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.36 r_work: 0.3036 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16330 Z= 0.141 Angle : 0.616 7.322 22254 Z= 0.309 Chirality : 0.044 0.181 2601 Planarity : 0.005 0.052 2787 Dihedral : 11.140 78.338 3126 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.61 % Allowed : 13.53 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.17), residues: 1992 helix: 1.27 (0.32), residues: 282 sheet: -0.56 (0.20), residues: 558 loop : -1.16 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 80 TYR 0.009 0.001 TYR L 38 PHE 0.018 0.002 PHE K 107 TRP 0.010 0.001 TRP K 115 HIS 0.003 0.001 HIS B 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16263) covalent geometry : angle 0.59020 / 0.30 (22077) SS BOND : bond 0.00265 / 0.15 ( 21) SS BOND : angle 1.54992 / 1.01 ( 42) hydrogen bonds : bond 0.04258 / 2.82 ( 600) hydrogen bonds : angle 6.02277 / 4.14 ( 1686) Misc. bond : bond 0.00158 / 0.08 ( 1) link_ALPHA1-3 : bond 0.00261 / 0.14 ( 6) link_ALPHA1-3 : angle 1.83684 / 1.01 ( 18) link_ALPHA1-6 : bond 0.00044 / 0.02 ( 3) link_ALPHA1-6 : angle 2.02845 / 1.08 ( 9) link_BETA1-4 : bond 0.00316 / 0.21 ( 15) link_BETA1-4 : angle 2.15279 / 1.32 ( 45) link_NAG-ASN : bond 0.00232 / 0.15 ( 21) link_NAG-ASN : angle 2.30351 / 1.44 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 182 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: G 17 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7547 (ttmm) REVERT: G 88 ARG cc_start: 0.8361 (mpp-170) cc_final: 0.7193 (ptt180) REVERT: G 183 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: I 458 GLU cc_start: 0.7515 (tt0) cc_final: 0.7169 (tt0) REVERT: J 106 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6213 (tm-30) REVERT: K 28 ARG cc_start: 0.7079 (ttp-170) cc_final: 0.6242 (mtp180) REVERT: K 126 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5724 (pp) REVERT: A 75 LYS cc_start: 0.8635 (mmtt) cc_final: 0.7402 (tttp) REVERT: A 88 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.7358 (ttt-90) REVERT: A 234 GLN cc_start: 0.8623 (mt0) cc_final: 0.8413 (mt0) REVERT: B 452 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: B 458 GLU cc_start: 0.7395 (tt0) cc_final: 0.6900 (tt0) REVERT: C 86 SER cc_start: 0.7260 (m) cc_final: 0.6539 (p) REVERT: D 27 GLN cc_start: 0.6510 (mm-40) cc_final: 0.6178 (mm-40) REVERT: E 38 LYS cc_start: 0.8405 (ttmt) cc_final: 0.7708 (tmtt) REVERT: E 336 LYS cc_start: 0.8350 (ptmt) cc_final: 0.8043 (ttpt) REVERT: F 401 SER cc_start: 0.8467 (m) cc_final: 0.8181 (p) REVERT: F 417 MET cc_start: 0.8408 (mmp) cc_final: 0.7966 (mmp) REVERT: F 458 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: H 86 SER cc_start: 0.6980 (m) cc_final: 0.6295 (p) REVERT: H 106 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.5907 (tm-30) outliers start: 61 outliers final: 28 residues processed: 232 average time/residue: 0.4898 time to fit residues: 128.0807 Evaluate side-chains 211 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain I residue 411 GLN Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 106 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 92 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 145 optimal weight: 0.0770 chunk 113 optimal weight: 0.2980 chunk 187 optimal weight: 10.0000 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 129 ASN G 148 ASN G 218 ASN G 234 GLN G 253 GLN I 400 ASN J 40 HIS K 66 ASN C 40 HIS ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN E 234 GLN F 398 ASN F 400 ASN H 40 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.180896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111696 restraints weight = 79431.394| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.21 r_work: 0.3041 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16330 Z= 0.092 Angle : 0.515 5.366 22254 Z= 0.257 Chirality : 0.041 0.222 2601 Planarity : 0.004 0.045 2787 Dihedral : 8.881 64.031 3096 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.96 % Allowed : 15.31 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.18), residues: 1992 helix: 2.32 (0.31), residues: 285 sheet: -0.47 (0.20), residues: 588 loop : -0.72 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 118 TYR 0.006 0.001 TYR G 310 PHE 0.014 0.001 PHE K 107 TRP 0.016 0.001 TRP K 115 HIS 0.002 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (16263) covalent geometry : angle 0.49470 / 0.25 (22077) SS BOND : bond 0.00224 / 0.13 ( 21) SS BOND : angle 1.16858 / 0.75 ( 42) hydrogen bonds : bond 0.03395 / 2.24 ( 600) hydrogen bonds : angle 5.36486 / 3.69 ( 1686) Misc. bond : bond 0.00130 / 0.07 ( 1) link_ALPHA1-3 : bond 0.00698 / 0.38 ( 6) link_ALPHA1-3 : angle 1.39215 / 0.74 ( 18) link_ALPHA1-6 : bond 0.00097 / 0.04 ( 3) link_ALPHA1-6 : angle 2.01814 / 1.13 ( 9) link_BETA1-4 : bond 0.00417 / 0.26 ( 15) link_BETA1-4 : angle 1.67412 / 1.02 ( 45) link_NAG-ASN : bond 0.00333 / 0.20 ( 21) link_NAG-ASN : angle 1.98909 / 1.29 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: G 17 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7514 (ttmm) REVERT: G 88 ARG cc_start: 0.8298 (mpp-170) cc_final: 0.7087 (ptt180) REVERT: G 168 THR cc_start: 0.8596 (p) cc_final: 0.8126 (t) REVERT: G 277 SER cc_start: 0.8545 (t) cc_final: 0.8322 (p) REVERT: I 411 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8545 (mp10) REVERT: I 458 GLU cc_start: 0.7461 (tt0) cc_final: 0.7155 (tt0) REVERT: J 26 SER cc_start: 0.5526 (m) cc_final: 0.4791 (p) REVERT: K 28 ARG cc_start: 0.6675 (ttp-170) cc_final: 0.5770 (mtp85) REVERT: A 75 LYS cc_start: 0.8603 (mmtt) cc_final: 0.7494 (tttm) REVERT: A 88 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7207 (ttt-90) REVERT: A 168 THR cc_start: 0.8597 (p) cc_final: 0.8132 (t) REVERT: A 183 GLU cc_start: 0.8051 (tp30) cc_final: 0.7762 (mm-30) REVERT: B 452 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: B 458 GLU cc_start: 0.7393 (tt0) cc_final: 0.6917 (tt0) REVERT: B 472 MET cc_start: 0.7126 (ptt) cc_final: 0.6488 (ppp) REVERT: E 38 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7658 (tmtt) REVERT: E 168 THR cc_start: 0.8641 (p) cc_final: 0.8171 (t) REVERT: F 401 SER cc_start: 0.8436 (m) cc_final: 0.8219 (p) REVERT: L 28 ARG cc_start: 0.6868 (ttt-90) cc_final: 0.6091 (mtp180) REVERT: L 125 GLU cc_start: 0.2757 (OUTLIER) cc_final: 0.2195 (mt-10) outliers start: 50 outliers final: 21 residues processed: 215 average time/residue: 0.5281 time to fit residues: 127.5851 Evaluate side-chains 194 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain I residue 411 GLN Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 158 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 125 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 148 ASN G 253 GLN A 148 ASN A 234 GLN E 148 ASN E 234 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110797 restraints weight = 78024.006| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 5.06 r_work: 0.3018 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16330 Z= 0.172 Angle : 0.573 5.726 22254 Z= 0.285 Chirality : 0.044 0.203 2601 Planarity : 0.004 0.054 2787 Dihedral : 8.291 59.376 3077 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.90 % Allowed : 15.96 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.18), residues: 1992 helix: 2.36 (0.31), residues: 285 sheet: -0.40 (0.20), residues: 612 loop : -0.56 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 118 TYR 0.013 0.001 TYR L 38 PHE 0.017 0.002 PHE K 107 TRP 0.006 0.001 TRP D 115 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (16263) covalent geometry : angle 0.54758 / 0.28 (22077) SS BOND : bond 0.00266 / 0.18 ( 21) SS BOND : angle 1.73596 / 1.12 ( 42) hydrogen bonds : bond 0.03895 / 2.55 ( 600) hydrogen bonds : angle 5.42147 / 3.72 ( 1686) Misc. bond : bond 0.00025 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00508 / 0.27 ( 6) link_ALPHA1-3 : angle 1.58998 / 0.86 ( 18) link_ALPHA1-6 : bond 0.00205 / 0.09 ( 3) link_ALPHA1-6 : angle 2.15292 / 1.21 ( 9) link_BETA1-4 : bond 0.00308 / 0.20 ( 15) link_BETA1-4 : angle 1.92204 / 1.18 ( 45) link_NAG-ASN : bond 0.00278 / 0.17 ( 21) link_NAG-ASN : angle 2.16725 / 1.37 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 17 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7512 (ttmm) REVERT: G 88 ARG cc_start: 0.8355 (mpp-170) cc_final: 0.7151 (ptt180) REVERT: I 458 GLU cc_start: 0.7465 (tt0) cc_final: 0.7182 (tt0) REVERT: J 26 SER cc_start: 0.5553 (m) cc_final: 0.4806 (p) REVERT: K 28 ARG cc_start: 0.6836 (ttp-170) cc_final: 0.5947 (mtp180) REVERT: A 75 LYS cc_start: 0.8597 (mmtt) cc_final: 0.7590 (tttm) REVERT: A 88 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.7304 (ttt-90) REVERT: A 183 GLU cc_start: 0.8054 (tp30) cc_final: 0.7827 (mm-30) REVERT: B 452 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: B 458 GLU cc_start: 0.7401 (tt0) cc_final: 0.6926 (tt0) REVERT: B 472 MET cc_start: 0.7050 (ptt) cc_final: 0.6493 (ppp) REVERT: E 38 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7752 (tptp) REVERT: F 455 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8110 (mt) REVERT: F 458 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: L 28 ARG cc_start: 0.6974 (ttt-90) cc_final: 0.6506 (mtp180) outliers start: 49 outliers final: 30 residues processed: 207 average time/residue: 0.5321 time to fit residues: 123.5155 Evaluate side-chains 200 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 20.0000 chunk 76 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 126 ASN G 129 ASN G 148 ASN K 106 HIS A 234 GLN D 106 HIS E 148 ASN E 234 GLN F 398 ASN L 106 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.178245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110247 restraints weight = 81395.912| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 4.41 r_work: 0.3017 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16330 Z= 0.215 Angle : 0.619 5.976 22254 Z= 0.309 Chirality : 0.046 0.208 2601 Planarity : 0.005 0.057 2787 Dihedral : 8.185 55.997 3074 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.08 % Allowed : 15.37 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 1992 helix: 2.17 (0.31), residues: 288 sheet: -0.30 (0.20), residues: 612 loop : -0.49 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 112 TYR 0.016 0.002 TYR L 38 PHE 0.021 0.002 PHE K 107 TRP 0.008 0.001 TRP C 110 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (16263) covalent geometry : angle 0.59174 / 0.30 (22077) SS BOND : bond 0.00321 / 0.22 ( 21) SS BOND : angle 2.12286 / 1.36 ( 42) hydrogen bonds : bond 0.04193 / 2.75 ( 600) hydrogen bonds : angle 5.52348 / 3.79 ( 1686) Misc. bond : bond 0.00006 / 0.00 ( 1) link_ALPHA1-3 : bond 0.00413 / 0.22 ( 6) link_ALPHA1-3 : angle 1.61425 / 0.88 ( 18) link_ALPHA1-6 : bond 0.00388 / 0.18 ( 3) link_ALPHA1-6 : angle 2.19681 / 1.24 ( 9) link_BETA1-4 : bond 0.00339 / 0.22 ( 15) link_BETA1-4 : angle 2.09884 / 1.29 ( 45) link_NAG-ASN : bond 0.00302 / 0.18 ( 21) link_NAG-ASN : angle 2.29008 / 1.42 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 166 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 17 LYS cc_start: 0.7944 (mtmm) cc_final: 0.7502 (ttmm) REVERT: G 88 ARG cc_start: 0.8363 (mpp-170) cc_final: 0.7149 (ptt180) REVERT: J 26 SER cc_start: 0.5610 (m) cc_final: 0.4880 (p) REVERT: K 28 ARG cc_start: 0.7008 (ttp-170) cc_final: 0.6127 (mtp180) REVERT: A 75 LYS cc_start: 0.8576 (mmtt) cc_final: 0.7503 (tttm) REVERT: A 88 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.7340 (ttt-90) REVERT: A 183 GLU cc_start: 0.8079 (tp30) cc_final: 0.7870 (mm-30) REVERT: B 452 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: B 458 GLU cc_start: 0.7452 (tt0) cc_final: 0.6968 (tt0) REVERT: C 86 SER cc_start: 0.7060 (m) cc_final: 0.6348 (p) REVERT: E 38 LYS cc_start: 0.8444 (ttmt) cc_final: 0.7848 (tptp) REVERT: F 417 MET cc_start: 0.8403 (mmp) cc_final: 0.7970 (mmp) REVERT: F 458 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7248 (tt0) REVERT: L 28 ARG cc_start: 0.6994 (ttt-90) cc_final: 0.6535 (mtp180) REVERT: L 125 GLU cc_start: 0.2634 (OUTLIER) cc_final: 0.2084 (mt-10) outliers start: 69 outliers final: 39 residues processed: 221 average time/residue: 0.5099 time to fit residues: 126.7078 Evaluate side-chains 200 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.0370 chunk 43 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 126 ASN G 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.182095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115040 restraints weight = 88633.083| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 4.68 r_work: 0.3069 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16330 Z= 0.095 Angle : 0.511 5.299 22254 Z= 0.254 Chirality : 0.041 0.216 2601 Planarity : 0.004 0.052 2787 Dihedral : 7.074 55.730 3074 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.84 % Allowed : 16.78 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 1992 helix: 2.82 (0.31), residues: 285 sheet: -0.19 (0.20), residues: 612 loop : -0.36 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 435 TYR 0.007 0.001 TYR E 310 PHE 0.014 0.001 PHE K 107 TRP 0.014 0.001 TRP K 115 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (16263) covalent geometry : angle 0.49112 / 0.25 (22077) SS BOND : bond 0.00382 / 0.27 ( 21) SS BOND : angle 1.21415 / 0.80 ( 42) hydrogen bonds : bond 0.03292 / 2.16 ( 600) hydrogen bonds : angle 5.15559 / 3.54 ( 1686) Misc. bond : bond 0.00024 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00727 / 0.39 ( 6) link_ALPHA1-3 : angle 1.43592 / 0.78 ( 18) link_ALPHA1-6 : bond 0.00038 / 0.02 ( 3) link_ALPHA1-6 : angle 2.13877 / 1.22 ( 9) link_BETA1-4 : bond 0.00384 / 0.24 ( 15) link_BETA1-4 : angle 1.65803 / 1.01 ( 45) link_NAG-ASN : bond 0.00277 / 0.16 ( 21) link_NAG-ASN : angle 1.89999 / 1.21 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: G 17 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7559 (ttmm) REVERT: G 88 ARG cc_start: 0.8333 (mpp-170) cc_final: 0.7101 (ttt-90) REVERT: G 168 THR cc_start: 0.8640 (p) cc_final: 0.8204 (t) REVERT: G 277 SER cc_start: 0.8612 (t) cc_final: 0.8380 (p) REVERT: J 26 SER cc_start: 0.5754 (m) cc_final: 0.5008 (p) REVERT: K 28 ARG cc_start: 0.6933 (ttp-170) cc_final: 0.6037 (mtp180) REVERT: A 75 LYS cc_start: 0.8558 (mmtt) cc_final: 0.7613 (tttm) REVERT: A 88 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7274 (ttt-90) REVERT: A 148 ASN cc_start: 0.7867 (t0) cc_final: 0.7596 (t160) REVERT: A 168 THR cc_start: 0.8623 (p) cc_final: 0.8138 (t) REVERT: B 452 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: B 458 GLU cc_start: 0.7491 (tt0) cc_final: 0.7031 (tt0) REVERT: E 38 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7785 (tptp) REVERT: E 168 THR cc_start: 0.8660 (p) cc_final: 0.8216 (t) REVERT: F 401 SER cc_start: 0.8441 (m) cc_final: 0.8236 (p) REVERT: F 458 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: H 106 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6211 (tm-30) REVERT: L 28 ARG cc_start: 0.6960 (ttt-90) cc_final: 0.6508 (mtp180) REVERT: L 125 GLU cc_start: 0.2716 (OUTLIER) cc_final: 0.2216 (mt-10) outliers start: 48 outliers final: 26 residues processed: 223 average time/residue: 0.5099 time to fit residues: 128.0257 Evaluate side-chains 210 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 190 optimal weight: 0.0670 chunk 31 optimal weight: 5.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 126 ASN G 129 ASN G 148 ASN G 234 GLN A 234 GLN E 148 ASN E 234 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.181947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114744 restraints weight = 81675.482| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.51 r_work: 0.3053 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16330 Z= 0.135 Angle : 0.543 5.842 22254 Z= 0.269 Chirality : 0.043 0.216 2601 Planarity : 0.004 0.054 2787 Dihedral : 6.896 55.522 3074 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.78 % Allowed : 17.14 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 1992 helix: 2.82 (0.31), residues: 285 sheet: -0.12 (0.20), residues: 612 loop : -0.29 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 112 TYR 0.011 0.001 TYR L 38 PHE 0.016 0.002 PHE K 107 TRP 0.010 0.001 TRP L 115 HIS 0.005 0.001 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (16263) covalent geometry : angle 0.51912 / 0.26 (22077) SS BOND : bond 0.00195 / 0.13 ( 21) SS BOND : angle 1.57825 / 1.03 ( 42) hydrogen bonds : bond 0.03558 / 2.32 ( 600) hydrogen bonds : angle 5.16770 / 3.55 ( 1686) Misc. bond : bond 0.00010 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00641 / 0.35 ( 6) link_ALPHA1-3 : angle 1.53066 / 0.84 ( 18) link_ALPHA1-6 : bond 0.00131 / 0.06 ( 3) link_ALPHA1-6 : angle 2.12135 / 1.22 ( 9) link_BETA1-4 : bond 0.00325 / 0.21 ( 15) link_BETA1-4 : angle 1.82161 / 1.11 ( 45) link_NAG-ASN : bond 0.00236 / 0.14 ( 21) link_NAG-ASN : angle 2.05028 / 1.30 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: G 17 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7579 (ttmm) REVERT: G 69 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7779 (ttm170) REVERT: G 88 ARG cc_start: 0.8333 (mpp-170) cc_final: 0.7103 (ttt-90) REVERT: G 168 THR cc_start: 0.8657 (p) cc_final: 0.8217 (t) REVERT: J 26 SER cc_start: 0.5748 (m) cc_final: 0.4999 (p) REVERT: K 28 ARG cc_start: 0.6862 (ttp-170) cc_final: 0.5998 (mtp180) REVERT: A 75 LYS cc_start: 0.8589 (mmtt) cc_final: 0.7594 (tttm) REVERT: A 88 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.7314 (ttt-90) REVERT: A 148 ASN cc_start: 0.7976 (t0) cc_final: 0.7691 (t160) REVERT: A 168 THR cc_start: 0.8685 (p) cc_final: 0.8182 (t) REVERT: B 452 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: B 458 GLU cc_start: 0.7459 (tt0) cc_final: 0.7018 (tt0) REVERT: E 38 LYS cc_start: 0.8429 (ttmt) cc_final: 0.7758 (tptp) REVERT: E 168 THR cc_start: 0.8702 (p) cc_final: 0.8248 (t) REVERT: F 401 SER cc_start: 0.8483 (m) cc_final: 0.8245 (p) REVERT: F 417 MET cc_start: 0.8377 (mmp) cc_final: 0.7906 (mmp) REVERT: F 458 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: H 86 SER cc_start: 0.7000 (m) cc_final: 0.6751 (m) REVERT: H 106 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6147 (tm-30) REVERT: L 28 ARG cc_start: 0.6961 (ttt-90) cc_final: 0.6496 (mtp180) REVERT: L 125 GLU cc_start: 0.2647 (OUTLIER) cc_final: 0.2166 (mt-10) outliers start: 47 outliers final: 30 residues processed: 211 average time/residue: 0.5205 time to fit residues: 123.7024 Evaluate side-chains 208 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain I residue 411 GLN Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 9 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 87 optimal weight: 0.0570 chunk 33 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 148 ASN B 398 ASN B 442 GLN E 148 ASN E 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112072 restraints weight = 71035.692| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.72 r_work: 0.3015 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16330 Z= 0.200 Angle : 0.603 6.542 22254 Z= 0.299 Chirality : 0.045 0.213 2601 Planarity : 0.004 0.058 2787 Dihedral : 7.146 56.508 3074 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.31 % Allowed : 16.78 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 1992 helix: 2.60 (0.31), residues: 285 sheet: -0.13 (0.20), residues: 612 loop : -0.32 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 265 TYR 0.015 0.002 TYR L 38 PHE 0.021 0.002 PHE K 107 TRP 0.010 0.001 TRP L 115 HIS 0.005 0.001 HIS E 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (16263) covalent geometry : angle 0.57602 / 0.29 (22077) SS BOND : bond 0.00324 / 0.22 ( 21) SS BOND : angle 2.01343 / 1.31 ( 42) hydrogen bonds : bond 0.04020 / 2.63 ( 600) hydrogen bonds : angle 5.35448 / 3.67 ( 1686) Misc. bond : bond 0.00002 / 0.00 ( 1) link_ALPHA1-3 : bond 0.00501 / 0.27 ( 6) link_ALPHA1-3 : angle 1.58765 / 0.87 ( 18) link_ALPHA1-6 : bond 0.00271 / 0.13 ( 3) link_ALPHA1-6 : angle 2.15204 / 1.25 ( 9) link_BETA1-4 : bond 0.00341 / 0.22 ( 15) link_BETA1-4 : angle 2.04201 / 1.25 ( 45) link_NAG-ASN : bond 0.00285 / 0.17 ( 21) link_NAG-ASN : angle 2.23110 / 1.39 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 17 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7530 (ttmm) REVERT: G 88 ARG cc_start: 0.8344 (mpp-170) cc_final: 0.7135 (ttt-90) REVERT: J 26 SER cc_start: 0.5738 (m) cc_final: 0.4988 (p) REVERT: K 28 ARG cc_start: 0.7073 (ttp-170) cc_final: 0.6212 (mtp180) REVERT: A 75 LYS cc_start: 0.8655 (mmtt) cc_final: 0.7602 (tttm) REVERT: A 88 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7341 (ttt-90) REVERT: B 452 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: B 458 GLU cc_start: 0.7455 (tt0) cc_final: 0.6999 (tt0) REVERT: C 86 SER cc_start: 0.6981 (m) cc_final: 0.6287 (p) REVERT: E 38 LYS cc_start: 0.8445 (ttmt) cc_final: 0.7830 (tptp) REVERT: E 80 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8604 (mtp180) REVERT: F 417 MET cc_start: 0.8441 (mmp) cc_final: 0.7890 (mmp) REVERT: F 458 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: H 86 SER cc_start: 0.6899 (m) cc_final: 0.6648 (m) REVERT: H 106 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6165 (tm-30) REVERT: L 125 GLU cc_start: 0.2552 (OUTLIER) cc_final: 0.2102 (mt-10) outliers start: 56 outliers final: 34 residues processed: 215 average time/residue: 0.5173 time to fit residues: 124.5356 Evaluate side-chains 207 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 33 optimal weight: 30.0000 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 87 optimal weight: 0.0170 chunk 130 optimal weight: 3.9990 chunk 116 optimal weight: 30.0000 chunk 159 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 234 GLN B 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112133 restraints weight = 78867.892| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.32 r_work: 0.3044 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16330 Z= 0.155 Angle : 0.563 6.088 22254 Z= 0.279 Chirality : 0.043 0.205 2601 Planarity : 0.004 0.056 2787 Dihedral : 6.872 58.013 3074 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.54 % Allowed : 17.55 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.18), residues: 1992 helix: 2.73 (0.31), residues: 285 sheet: -0.09 (0.20), residues: 612 loop : -0.29 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 435 TYR 0.011 0.001 TYR L 38 PHE 0.018 0.002 PHE K 107 TRP 0.014 0.001 TRP K 115 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (16263) covalent geometry : angle 0.53857 / 0.27 (22077) SS BOND : bond 0.00226 / 0.16 ( 21) SS BOND : angle 1.64943 / 1.08 ( 42) hydrogen bonds : bond 0.03733 / 2.44 ( 600) hydrogen bonds : angle 5.27049 / 3.61 ( 1686) Misc. bond : bond 0.00001 / 0.00 ( 1) link_ALPHA1-3 : bond 0.00579 / 0.31 ( 6) link_ALPHA1-3 : angle 1.51671 / 0.83 ( 18) link_ALPHA1-6 : bond 0.00138 / 0.06 ( 3) link_ALPHA1-6 : angle 2.09278 / 1.21 ( 9) link_BETA1-4 : bond 0.00331 / 0.22 ( 15) link_BETA1-4 : angle 1.90792 / 1.17 ( 45) link_NAG-ASN : bond 0.00225 / 0.14 ( 21) link_NAG-ASN : angle 2.11824 / 1.32 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 17 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7565 (ttmm) REVERT: G 88 ARG cc_start: 0.8357 (mpp-170) cc_final: 0.7131 (ttt-90) REVERT: G 168 THR cc_start: 0.8645 (p) cc_final: 0.8191 (t) REVERT: J 26 SER cc_start: 0.5757 (m) cc_final: 0.5015 (p) REVERT: K 28 ARG cc_start: 0.7062 (ttp-170) cc_final: 0.6190 (mtp180) REVERT: A 75 LYS cc_start: 0.8654 (mmtt) cc_final: 0.7633 (tttm) REVERT: A 88 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.7331 (ttt-90) REVERT: B 448 LEU cc_start: 0.8350 (tt) cc_final: 0.8143 (tp) REVERT: B 452 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7507 (mm-30) REVERT: B 458 GLU cc_start: 0.7459 (tt0) cc_final: 0.7007 (tt0) REVERT: C 86 SER cc_start: 0.6958 (m) cc_final: 0.6269 (p) REVERT: E 38 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7850 (tptp) REVERT: E 80 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8606 (mtp180) REVERT: F 401 SER cc_start: 0.8497 (m) cc_final: 0.8289 (p) REVERT: F 417 MET cc_start: 0.8415 (mmp) cc_final: 0.7899 (mmp) REVERT: F 458 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: H 86 SER cc_start: 0.6933 (m) cc_final: 0.6680 (m) REVERT: H 106 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6088 (tm-30) REVERT: L 125 GLU cc_start: 0.2615 (OUTLIER) cc_final: 0.2162 (mt-10) outliers start: 43 outliers final: 35 residues processed: 209 average time/residue: 0.5141 time to fit residues: 120.9804 Evaluate side-chains 213 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 165 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 173 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 148 ASN B 442 GLN E 148 ASN E 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.179482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113014 restraints weight = 65991.413| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.56 r_work: 0.3030 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16330 Z= 0.165 Angle : 0.570 5.685 22254 Z= 0.283 Chirality : 0.044 0.202 2601 Planarity : 0.004 0.057 2787 Dihedral : 6.772 59.831 3074 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.72 % Allowed : 17.49 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 1992 helix: 2.73 (0.30), residues: 285 sheet: -0.08 (0.20), residues: 612 loop : -0.27 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 80 TYR 0.012 0.001 TYR K 38 PHE 0.019 0.002 PHE K 107 TRP 0.015 0.001 TRP K 115 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (16263) covalent geometry : angle 0.54565 / 0.28 (22077) SS BOND : bond 0.00255 / 0.18 ( 21) SS BOND : angle 1.70486 / 1.11 ( 42) hydrogen bonds : bond 0.03783 / 2.47 ( 600) hydrogen bonds : angle 5.27625 / 3.62 ( 1686) Misc. bond : bond 0.00004 / 0.00 ( 1) link_ALPHA1-3 : bond 0.00568 / 0.31 ( 6) link_ALPHA1-3 : angle 1.51269 / 0.83 ( 18) link_ALPHA1-6 : bond 0.00095 / 0.04 ( 3) link_ALPHA1-6 : angle 2.04934 / 1.19 ( 9) link_BETA1-4 : bond 0.00327 / 0.21 ( 15) link_BETA1-4 : angle 1.95889 / 1.20 ( 45) link_NAG-ASN : bond 0.00235 / 0.14 ( 21) link_NAG-ASN : angle 2.13559 / 1.33 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 17 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7551 (ttmm) REVERT: G 88 ARG cc_start: 0.8338 (mpp-170) cc_final: 0.7131 (ttt-90) REVERT: J 26 SER cc_start: 0.5739 (m) cc_final: 0.4999 (p) REVERT: K 28 ARG cc_start: 0.7050 (ttp-170) cc_final: 0.6176 (mtp180) REVERT: A 75 LYS cc_start: 0.8650 (mmtt) cc_final: 0.7597 (tttm) REVERT: A 88 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7294 (ttt-90) REVERT: B 452 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7438 (mm-30) REVERT: B 458 GLU cc_start: 0.7440 (tt0) cc_final: 0.6998 (tt0) REVERT: C 86 SER cc_start: 0.6973 (m) cc_final: 0.6275 (p) REVERT: E 38 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7839 (tptp) REVERT: E 80 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8587 (mtp180) REVERT: F 392 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.7119 (mp) REVERT: F 458 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: H 86 SER cc_start: 0.6865 (m) cc_final: 0.6615 (m) REVERT: H 106 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6080 (tm-30) REVERT: L 125 GLU cc_start: 0.2522 (OUTLIER) cc_final: 0.2067 (mt-10) outliers start: 46 outliers final: 36 residues processed: 204 average time/residue: 0.5197 time to fit residues: 119.1662 Evaluate side-chains 209 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 181 CYS Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain I residue 401 SER Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 90 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 109 optimal weight: 0.0170 chunk 138 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 161 optimal weight: 30.0000 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 126 ASN G 129 ASN B 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.182529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117011 restraints weight = 71508.569| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.84 r_work: 0.3076 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16330 Z= 0.089 Angle : 0.495 5.990 22254 Z= 0.247 Chirality : 0.041 0.179 2601 Planarity : 0.004 0.053 2787 Dihedral : 6.039 56.342 3073 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.25 % Allowed : 17.97 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 1992 helix: 3.16 (0.31), residues: 285 sheet: 0.01 (0.20), residues: 612 loop : -0.19 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 88 TYR 0.008 0.001 TYR G 310 PHE 0.014 0.001 PHE K 107 TRP 0.025 0.001 TRP K 115 HIS 0.005 0.001 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (16263) covalent geometry : angle 0.47512 / 0.24 (22077) SS BOND : bond 0.00130 / 0.08 ( 21) SS BOND : angle 1.16914 / 0.76 ( 42) hydrogen bonds : bond 0.03116 / 2.03 ( 600) hydrogen bonds : angle 4.99612 / 3.44 ( 1686) Misc. bond : bond 0.00015 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00793 / 0.43 ( 6) link_ALPHA1-3 : angle 1.38539 / 0.75 ( 18) link_ALPHA1-6 : bond 0.00239 / 0.11 ( 3) link_ALPHA1-6 : angle 1.87476 / 1.09 ( 9) link_BETA1-4 : bond 0.00390 / 0.24 ( 15) link_BETA1-4 : angle 1.61523 / 0.98 ( 45) link_NAG-ASN : bond 0.00267 / 0.15 ( 21) link_NAG-ASN : angle 1.86778 / 1.18 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7176.04 seconds wall clock time: 122 minutes 31.98 seconds (7351.98 seconds total)