Starting phenix.real_space_refine on Sun Oct 25 16:17:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/43sn_82114/10_2026/43sn_82114.cif Found real_map, /net/cci-nas-00/data/ceres_data/43sn_82114/10_2026/43sn_82114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/43sn_82114/10_2026/43sn_82114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/43sn_82114/10_2026/43sn_82114.map" model { file = "/net/cci-nas-00/data/ceres_data/43sn_82114/10_2026/43sn_82114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/43sn_82114/10_2026/43sn_82114.cif" } resolution = 2.71 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= 0.008 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 11055 2.51 5 N 2765 2.21 5 O 3090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17045 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3215 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3208 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 399, 3208 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 3288 Chain: "B" Number of atoms: 123 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Conformer: "B" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} bond proxies already assigned to first conformer: 101 Chain: "C" Number of atoms: 3215 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3208 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 399, 3208 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 3288 Chain: "D" Number of atoms: 123 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Conformer: "B" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} bond proxies already assigned to first conformer: 101 Chain: "E" Number of atoms: 3215 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3208 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 399, 3208 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 3288 Chain: "F" Number of atoms: 123 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Conformer: "B" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} bond proxies already assigned to first conformer: 101 Chain: "G" Number of atoms: 3215 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3208 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 399, 3208 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 3288 Chain: "H" Number of atoms: 123 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Conformer: "B" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} bond proxies already assigned to first conformer: 101 Chain: "I" Number of atoms: 3215 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3208 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 399, 3208 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 3288 Chain: "J" Number of atoms: 123 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Conformer: "B" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} bond proxies already assigned to first conformer: 101 Chain: "K" 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: "L" 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: "M" 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: "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: 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: "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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.21, per 1000 atoms: 0.36 Number of scatterers: 17045 At special positions: 0 Unit cell: (96.3, 96.3, 165.85, 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 135 16.00 O 3090 8.00 N 2765 7.00 C 11055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.05 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 16 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 10 " distance=2.03 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 16 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 10 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.05 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.02 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 10 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 212 " - pdb=" SG CYS G 213 " distance=2.07 Simple disulfide: pdb=" SG CYS H 2 " - pdb=" SG CYS H 16 " distance=2.03 Simple disulfide: pdb=" SG CYS H 4 " - pdb=" SG CYS H 10 " distance=2.03 Simple disulfide: pdb=" SG CYS I 150 " - pdb=" SG CYS I 164 " distance=2.03 Simple disulfide: pdb=" SG CYS I 212 " - pdb=" SG CYS I 213 " distance=2.05 Simple disulfide: pdb=" SG CYS J 2 " - pdb=" SG CYS J 16 " distance=2.03 Simple disulfide: pdb=" SG CYS J 4 " - pdb=" SG CYS J 10 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 601 " - " ASN A 90 " " NAG C 601 " - " ASN C 90 " " NAG E 601 " - " ASN E 90 " " NAG G 601 " - " ASN G 90 " " NAG I 601 " - " ASN I 90 " " NAG K 1 " - " ASN A 46 " " NAG L 1 " - " ASN A 133 " " NAG M 1 " - " ASN C 46 " " NAG N 1 " - " ASN C 133 " " NAG O 1 " - " ASN E 46 " " NAG P 1 " - " ASN E 133 " " NAG Q 1 " - " ASN G 46 " " NAG R 1 " - " ASN G 133 " " NAG S 1 " - " ASN I 46 " " NAG T 1 " - " ASN I 133 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 1.0 seconds 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 43.2% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.610A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 260 through 280 Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 431 through 489 removed outlier: 3.924A pdb=" N LYS A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 502 Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.555A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 237 through 250 Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 260 through 280 Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 431 through 490 removed outlier: 3.894A pdb=" N LYS C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 502 Processing helix chain 'D' and resid 8 through 13 removed outlier: 3.599A pdb=" N ALA D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.629A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 237 through 250 Processing helix chain 'E' and resid 251 through 254 Processing helix chain 'E' and resid 260 through 280 Processing helix chain 'E' and resid 291 through 319 Processing helix chain 'E' and resid 328 through 336 Processing helix chain 'E' and resid 337 through 344 Processing helix chain 'E' and resid 431 through 489 removed outlier: 3.865A pdb=" N LYS E 435 " --> pdb=" O PRO E 431 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE E 436 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 502 Processing helix chain 'F' and resid 8 through 13 removed outlier: 3.642A pdb=" N ALA F 12 " --> pdb=" O GLY F 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 34 removed outlier: 3.558A pdb=" N VAL G 34 " --> pdb=" O TYR G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 237 Processing helix chain 'G' and resid 237 through 250 Processing helix chain 'G' and resid 251 through 254 Processing helix chain 'G' and resid 260 through 280 Processing helix chain 'G' and resid 291 through 319 Processing helix chain 'G' and resid 328 through 336 Processing helix chain 'G' and resid 338 through 344 Processing helix chain 'G' and resid 431 through 489 removed outlier: 3.853A pdb=" N LYS G 435 " --> pdb=" O PRO G 431 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE G 436 " --> pdb=" O ASP G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 502 Processing helix chain 'H' and resid 8 through 13 Processing helix chain 'I' and resid 24 through 34 removed outlier: 3.592A pdb=" N VAL I 34 " --> pdb=" O TYR I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 237 Processing helix chain 'I' and resid 237 through 250 Processing helix chain 'I' and resid 251 through 254 Processing helix chain 'I' and resid 260 through 280 Processing helix chain 'I' and resid 291 through 319 Processing helix chain 'I' and resid 328 through 336 Processing helix chain 'I' and resid 338 through 344 Processing helix chain 'I' and resid 431 through 489 removed outlier: 3.922A pdb=" N LYS I 435 " --> pdb=" O PRO I 431 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE I 436 " --> pdb=" O ASP I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 502 Processing helix chain 'J' and resid 8 through 13 removed outlier: 3.781A pdb=" N ALA J 12 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 102 removed outlier: 4.353A pdb=" N HIS A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 102 removed outlier: 4.353A pdb=" N HIS A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 71 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL A 65 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A 73 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP A 77 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU A 59 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN A 79 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU A 57 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N SER A 81 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE A 55 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR A 83 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL A 53 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.896A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.896A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 99 through 102 removed outlier: 4.380A pdb=" N HIS C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 102 removed outlier: 4.380A pdb=" N HIS C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 71 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL C 65 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR C 73 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TRP C 77 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU C 59 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN C 79 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU C 57 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER C 81 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE C 55 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N THR C 83 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL C 53 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.928A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.928A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 99 through 102 removed outlier: 4.370A pdb=" N HIS E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 99 through 102 removed outlier: 4.370A pdb=" N HIS E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLN E 79 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N SER E 58 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER E 81 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N SER E 56 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N THR E 83 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N TYR E 54 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.943A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.943A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 99 through 102 removed outlier: 4.254A pdb=" N HIS G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 99 through 102 removed outlier: 4.254A pdb=" N HIS G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 71 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL G 65 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR G 73 " --> pdb=" O MET G 63 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TRP G 77 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU G 59 " --> pdb=" O TRP G 77 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN G 79 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU G 57 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER G 81 " --> pdb=" O PHE G 55 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N PHE G 55 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR G 83 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL G 53 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU G 51 " --> pdb=" O ASP G 179 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLN G 181 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL G 53 " --> pdb=" O GLN G 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 112 through 114 removed outlier: 4.790A pdb=" N SER G 170 " --> pdb=" O PRO G 218 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR G 225 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 112 through 114 removed outlier: 4.790A pdb=" N SER G 170 " --> pdb=" O PRO G 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 99 through 102 removed outlier: 4.327A pdb=" N HIS I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 99 through 102 removed outlier: 4.327A pdb=" N HIS I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL I 71 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL I 65 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR I 73 " --> pdb=" O MET I 63 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP I 77 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU I 59 " --> pdb=" O TRP I 77 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN I 79 " --> pdb=" O LEU I 57 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 57 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N SER I 81 " --> pdb=" O PHE I 55 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE I 55 " --> pdb=" O SER I 81 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR I 83 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL I 53 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 112 through 114 removed outlier: 4.823A pdb=" N SER I 170 " --> pdb=" O PRO I 218 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR I 225 " --> pdb=" O VAL I 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 112 through 114 removed outlier: 4.823A pdb=" N SER I 170 " --> pdb=" O PRO I 218 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2841 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: 2.96 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2668 1.32 - 1.45: 5026 1.45 - 1.58: 9641 1.58 - 1.72: 0 1.72 - 1.85: 190 Bond restraints: 17525 Sorted by residual: bond pdb=" C7 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.346 1.460 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C7 NAG C 601 " pdb=" N2 NAG C 601 " ideal model delta sigma weight residual 1.346 1.459 -0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C7 NAG O 2 " pdb=" N2 NAG O 2 " ideal model delta sigma weight residual 1.346 1.459 -0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" C7 NAG Q 2 " pdb=" N2 NAG Q 2 " ideal model delta sigma weight residual 1.346 1.459 -0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" C7 NAG S 2 " pdb=" N2 NAG S 2 " ideal model delta sigma weight residual 1.346 1.459 -0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 17520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 23336 2.02 - 4.04: 433 4.04 - 6.06: 114 6.06 - 8.07: 0 8.07 - 10.09: 2 Bond angle restraints: 23885 Sorted by residual: angle pdb=" N GLU C 438 " pdb=" CA GLU C 438 " pdb=" CB GLU C 438 " ideal model delta sigma weight residual 110.16 115.30 -5.14 1.48e+00 4.57e-01 1.21e+01 angle pdb=" CB MET I 301 " pdb=" CG MET I 301 " pdb=" SD MET I 301 " ideal model delta sigma weight residual 112.70 102.61 10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CB MET C 301 " pdb=" CG MET C 301 " pdb=" SD MET C 301 " ideal model delta sigma weight residual 112.70 103.84 8.86 3.00e+00 1.11e-01 8.73e+00 angle pdb=" N VAL G 154 " pdb=" CA VAL G 154 " pdb=" C VAL G 154 " ideal model delta sigma weight residual 111.88 108.81 3.07 1.06e+00 8.90e-01 8.38e+00 angle pdb=" C PRO C 491 " pdb=" N ASN C 492 " pdb=" CA ASN C 492 " ideal model delta sigma weight residual 121.54 126.45 -4.91 1.91e+00 2.74e-01 6.61e+00 ... (remaining 23880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 9753 17.73 - 35.47: 726 35.47 - 53.20: 106 53.20 - 70.93: 33 70.93 - 88.67: 12 Dihedral angle restraints: 10630 sinusoidal: 4540 harmonic: 6090 Sorted by residual: dihedral pdb=" CB CYS H 2 " pdb=" SG CYS H 2 " pdb=" SG CYS H 16 " pdb=" CB CYS H 16 " ideal model delta sinusoidal sigma weight residual 93.00 -178.33 -88.67 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS B 2 " pdb=" SG CYS B 2 " pdb=" SG CYS B 16 " pdb=" CB CYS B 16 " ideal model delta sinusoidal sigma weight residual 93.00 -178.62 -88.38 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CB CYS J 2 " pdb=" SG CYS J 2 " pdb=" SG CYS J 16 " pdb=" CB CYS J 16 " ideal model delta sinusoidal sigma weight residual 93.00 178.90 -85.90 1 1.00e+01 1.00e-02 8.91e+01 ... (remaining 10627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2026 0.043 - 0.085: 514 0.085 - 0.128: 124 0.128 - 0.170: 40 0.170 - 0.213: 1 Chirality restraints: 2705 Sorted by residual: chirality pdb=" CB ILE G 201 " pdb=" CA ILE G 201 " pdb=" CG1 ILE G 201 " pdb=" CG2 ILE G 201 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE C 201 " pdb=" CA ILE C 201 " pdb=" CG1 ILE C 201 " pdb=" CG2 ILE C 201 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CB VAL E 154 " pdb=" CA VAL E 154 " pdb=" CG1 VAL E 154 " pdb=" CG2 VAL E 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 2702 not shown) Planarity restraints: 2975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 191 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO G 192 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO G 192 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 192 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 290 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO I 291 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO I 291 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 291 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET G 327 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO G 328 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 328 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 328 " 0.032 5.00e-02 4.00e+02 ... (remaining 2972 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3233 2.78 - 3.31: 15930 3.31 - 3.84: 29452 3.84 - 4.37: 34083 4.37 - 4.90: 60090 Nonbonded interactions: 142788 Sorted by model distance: nonbonded pdb=" O SER C 172 " pdb=" NH2 ARG E 101 " model vdw 2.247 3.120 nonbonded pdb=" O ASN G 193 " pdb=" NH1 ARG G 229 " model vdw 2.256 3.120 nonbonded pdb=" NH2 ARG E 42 " pdb=" O ASP E 47 " model vdw 2.256 3.120 nonbonded pdb=" OD2 ASP I 186 " pdb=" OG SER I 188 " model vdw 2.278 3.040 nonbonded pdb=" O ASN E 69 " pdb=" NE2 GLN G 61 " model vdw 2.287 3.120 ... (remaining 142783 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 23 through 136 or resid 138 through 601)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 601)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 601)) selection = (chain 'G' and (resid 23 through 136 or resid 138 through 601)) selection = (chain 'I' and (resid 23 through 136 or resid 138 through 601)) } ncs_group { reference = (chain 'B' and (resid 1 through 8 or resid 10 through 17)) selection = (chain 'D' and (resid 1 through 8 or resid 10 through 17)) selection = (chain 'F' and (resid 1 through 8 or resid 10 through 17)) selection = (chain 'H' and (resid 1 through 8 or resid 10 through 17)) selection = (chain 'J' and (resid 1 through 8 or resid 10 through 17)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.37 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.310 Find NCS groups from input model: 0.570 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:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.008 0.114 17570 Z= 0.390 Angle : 0.670 10.093 24000 Z= 0.314 Chirality : 0.042 0.213 2705 Planarity : 0.004 0.061 2960 Dihedral : 12.501 83.645 6650 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.96 (0.18), residues: 2060 helix: 1.75 (0.17), residues: 850 sheet: 0.29 (0.24), residues: 450 loop : -0.33 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 13 TYR 0.011 0.001 TYR I 210 PHE 0.013 0.001 PHE I 275 TRP 0.009 0.001 TRP E 341 HIS 0.003 0.001 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.39 (17525) covalent geometry : angle 0.66039 / 0.31 (23885) SS BOND : bond 0.01148 / 0.86 ( 20) SS BOND : angle 2.33005 / 1.49 ( 40) hydrogen bonds : bond 0.10337 / 6.95 ( 863) hydrogen bonds : angle 5.91568 / 4.12 ( 2841) link_BETA1-4 : bond 0.00273 / 0.17 ( 10) link_BETA1-4 : angle 0.82675 / 0.55 ( 30) link_NAG-ASN : bond 0.00077 / 0.04 ( 15) link_NAG-ASN : angle 1.62534 / 1.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.684 Fit side-chains REVERT: A 341 TRP cc_start: 0.8223 (t60) cc_final: 0.7679 (t60) REVERT: A 342 PHE cc_start: 0.7383 (t80) cc_final: 0.6168 (m-10) REVERT: C 341 TRP cc_start: 0.8068 (t60) cc_final: 0.7845 (t60) REVERT: E 208 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6899 (mpt90) REVERT: E 342 PHE cc_start: 0.7100 (t80) cc_final: 0.5922 (m-10) REVERT: G 61 GLN cc_start: 0.7962 (tt0) cc_final: 0.7516 (tt0) REVERT: G 66 ASP cc_start: 0.7918 (t70) cc_final: 0.6966 (t0) REVERT: G 68 LYS cc_start: 0.8655 (tttm) cc_final: 0.8294 (tttp) REVERT: G 69 ASN cc_start: 0.8468 (m110) cc_final: 0.8224 (m110) REVERT: G 342 PHE cc_start: 0.7428 (t80) cc_final: 0.5979 (m-10) REVERT: I 69 ASN cc_start: 0.8651 (m110) cc_final: 0.8449 (m110) REVERT: I 341 TRP cc_start: 0.8230 (t60) cc_final: 0.7853 (t60) outliers start: 0 outliers final: 4 residues processed: 215 average time/residue: 0.5644 time to fit residues: 136.4506 Evaluate side-chains 161 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain G residue 480 ILE Chi-restraints excluded: chain I residue 480 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 77, 122, 91] chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.088660 restraints weight = 52297.932| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.57 r_work: 0.2904 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17570 Z= 0.121 Angle : 0.552 8.839 24000 Z= 0.276 Chirality : 0.041 0.202 2705 Planarity : 0.004 0.050 2960 Dihedral : 6.278 53.950 2798 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.65 % Allowed : 6.76 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 2060 helix: 1.59 (0.17), residues: 890 sheet: 0.35 (0.25), residues: 410 loop : -0.15 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 229 TYR 0.008 0.001 TYR C 442 PHE 0.011 0.001 PHE I 275 TRP 0.011 0.001 TRP E 82 HIS 0.003 0.001 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (17525) covalent geometry : angle 0.52680 / 0.27 (23885) SS BOND : bond 0.01023 / 0.65 ( 20) SS BOND : angle 3.32920 / 2.21 ( 40) hydrogen bonds : bond 0.03879 / 2.52 ( 863) hydrogen bonds : angle 4.77809 / 3.33 ( 2841) link_BETA1-4 : bond 0.00303 / 0.20 ( 10) link_BETA1-4 : angle 1.19605 / 0.79 ( 30) link_NAG-ASN : bond 0.00124 / 0.08 ( 15) link_NAG-ASN : angle 2.05733 / 1.51 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8428 (m110) cc_final: 0.8145 (m110) REVERT: A 197 ASP cc_start: 0.8519 (t70) cc_final: 0.8237 (t0) REVERT: A 341 TRP cc_start: 0.8277 (t60) cc_final: 0.7801 (t60) REVERT: A 342 PHE cc_start: 0.7590 (t80) cc_final: 0.6200 (m-10) REVERT: C 277 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7552 (tp) REVERT: C 341 TRP cc_start: 0.8217 (t60) cc_final: 0.7938 (t60) REVERT: E 116 ASN cc_start: 0.8482 (m110) cc_final: 0.8243 (m110) REVERT: E 208 ARG cc_start: 0.7670 (mmt180) cc_final: 0.7293 (mmt180) REVERT: E 277 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7190 (tp) REVERT: E 342 PHE cc_start: 0.7210 (t80) cc_final: 0.5922 (m-10) REVERT: G 66 ASP cc_start: 0.8076 (t70) cc_final: 0.7231 (t0) REVERT: G 68 LYS cc_start: 0.8844 (tttm) cc_final: 0.8515 (tttp) REVERT: G 69 ASN cc_start: 0.8737 (m110) cc_final: 0.8439 (m110) REVERT: G 342 PHE cc_start: 0.7533 (t80) cc_final: 0.5993 (m-10) REVERT: I 341 TRP cc_start: 0.8237 (t60) cc_final: 0.7882 (t60) outliers start: 12 outliers final: 1 residues processed: 180 average time/residue: 0.5599 time to fit residues: 113.0963 Evaluate side-chains 159 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 473 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [24, 181, 180, 50, 30, 15, 105, 67, 152, 197, 35] chunk 24 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 197 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.088405 restraints weight = 50424.737| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.48 r_work: 0.2906 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17570 Z= 0.123 Angle : 0.525 8.221 24000 Z= 0.261 Chirality : 0.040 0.192 2705 Planarity : 0.003 0.044 2960 Dihedral : 5.374 51.609 2790 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.71 % Allowed : 8.01 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.18), residues: 2060 helix: 1.66 (0.16), residues: 890 sheet: 0.49 (0.26), residues: 400 loop : -0.23 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 101 TYR 0.013 0.001 TYR I 233 PHE 0.011 0.001 PHE I 275 TRP 0.009 0.001 TRP E 82 HIS 0.003 0.001 HIS E 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (17525) covalent geometry : angle 0.49971 / 0.25 (23885) SS BOND : bond 0.00844 / 0.55 ( 20) SS BOND : angle 3.18153 / 2.04 ( 40) hydrogen bonds : bond 0.03767 / 2.44 ( 863) hydrogen bonds : angle 4.54600 / 3.17 ( 2841) link_BETA1-4 : bond 0.00223 / 0.15 ( 10) link_BETA1-4 : angle 1.19582 / 0.80 ( 30) link_NAG-ASN : bond 0.00135 / 0.09 ( 15) link_NAG-ASN : angle 2.06298 / 1.52 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8513 (m110) cc_final: 0.8265 (m110) REVERT: A 197 ASP cc_start: 0.8522 (t70) cc_final: 0.8287 (t0) REVERT: A 341 TRP cc_start: 0.8306 (t60) cc_final: 0.7779 (t60) REVERT: A 342 PHE cc_start: 0.7645 (t80) cc_final: 0.6126 (m-10) REVERT: C 238 LEU cc_start: 0.7503 (tp) cc_final: 0.7242 (mm) REVERT: C 341 TRP cc_start: 0.8321 (t60) cc_final: 0.7938 (t60) REVERT: C 438 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6481 (mm-30) REVERT: E 116 ASN cc_start: 0.8519 (m110) cc_final: 0.8281 (m110) REVERT: E 197 ASP cc_start: 0.8257 (t70) cc_final: 0.7974 (t0) REVERT: E 208 ARG cc_start: 0.7591 (mmt180) cc_final: 0.7138 (mmt-90) REVERT: E 277 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7209 (tp) REVERT: E 342 PHE cc_start: 0.7277 (t80) cc_final: 0.5926 (m-10) REVERT: G 64 ASP cc_start: 0.8191 (t0) cc_final: 0.7902 (t0) REVERT: G 66 ASP cc_start: 0.7910 (t70) cc_final: 0.6940 (t0) REVERT: G 68 LYS cc_start: 0.8823 (tttm) cc_final: 0.8483 (tttp) REVERT: G 69 ASN cc_start: 0.8699 (m110) cc_final: 0.8313 (m110) REVERT: G 197 ASP cc_start: 0.8483 (t70) cc_final: 0.8174 (t0) REVERT: G 342 PHE cc_start: 0.7550 (t80) cc_final: 0.6137 (m-10) REVERT: I 64 ASP cc_start: 0.8090 (t70) cc_final: 0.7880 (t0) REVERT: I 283 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7353 (ttp) REVERT: I 313 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.6741 (mp) REVERT: I 341 TRP cc_start: 0.8279 (t60) cc_final: 0.7884 (t60) REVERT: I 468 ASP cc_start: 0.7281 (m-30) cc_final: 0.6983 (m-30) outliers start: 13 outliers final: 3 residues processed: 179 average time/residue: 0.5510 time to fit residues: 111.0108 Evaluate side-chains 169 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 476 SER Chi-restraints excluded: chain G residue 480 ILE Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 313 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [103, 101, 13, 185, 8, 60, 75, 81, 74, 188, 173] chunk 103 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 74 optimal weight: 0.0050 chunk 188 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN E 69 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.094260 restraints weight = 61142.112| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.99 r_work: 0.3009 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17570 Z= 0.111 Angle : 0.507 8.366 24000 Z= 0.252 Chirality : 0.040 0.185 2705 Planarity : 0.003 0.041 2960 Dihedral : 4.642 42.395 2790 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.87 % Allowed : 8.45 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.18), residues: 2060 helix: 1.73 (0.16), residues: 895 sheet: 0.49 (0.26), residues: 410 loop : -0.22 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.007 0.001 TYR C 442 PHE 0.009 0.001 PHE C 275 TRP 0.008 0.001 TRP E 82 HIS 0.002 0.000 HIS E 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (17525) covalent geometry : angle 0.48301 / 0.24 (23885) SS BOND : bond 0.00813 / 0.54 ( 20) SS BOND : angle 3.06215 / 1.94 ( 40) hydrogen bonds : bond 0.03541 / 2.30 ( 863) hydrogen bonds : angle 4.40806 / 3.07 ( 2841) link_BETA1-4 : bond 0.00248 / 0.17 ( 10) link_BETA1-4 : angle 1.04759 / 0.70 ( 30) link_NAG-ASN : bond 0.00092 / 0.06 ( 15) link_NAG-ASN : angle 2.01228 / 1.48 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8501 (m110) cc_final: 0.8218 (m110) REVERT: A 341 TRP cc_start: 0.8278 (t60) cc_final: 0.7683 (t60) REVERT: A 342 PHE cc_start: 0.7668 (t80) cc_final: 0.6021 (m-10) REVERT: C 341 TRP cc_start: 0.8268 (t60) cc_final: 0.7896 (t60) REVERT: C 438 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6501 (mm-30) REVERT: E 116 ASN cc_start: 0.8454 (m110) cc_final: 0.8209 (m110) REVERT: E 197 ASP cc_start: 0.8208 (t70) cc_final: 0.7825 (t0) REVERT: E 208 ARG cc_start: 0.7575 (mmt180) cc_final: 0.7031 (mmt-90) REVERT: E 277 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7027 (tp) REVERT: E 288 ASP cc_start: 0.7588 (p0) cc_final: 0.7382 (t0) REVERT: E 342 PHE cc_start: 0.7378 (t80) cc_final: 0.5955 (m-10) REVERT: G 64 ASP cc_start: 0.8171 (t0) cc_final: 0.7908 (t0) REVERT: G 66 ASP cc_start: 0.7799 (t70) cc_final: 0.6720 (t0) REVERT: G 68 LYS cc_start: 0.8721 (tttm) cc_final: 0.8380 (tttp) REVERT: G 69 ASN cc_start: 0.8646 (m110) cc_final: 0.8179 (m110) REVERT: G 197 ASP cc_start: 0.8408 (t70) cc_final: 0.8122 (t0) REVERT: G 342 PHE cc_start: 0.7529 (t80) cc_final: 0.6125 (m-10) REVERT: I 313 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.6732 (mp) REVERT: I 341 TRP cc_start: 0.8353 (t60) cc_final: 0.7901 (t60) outliers start: 16 outliers final: 8 residues processed: 186 average time/residue: 0.5348 time to fit residues: 112.5879 Evaluate side-chains 176 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 476 SER Chi-restraints excluded: chain G residue 226 MET Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain G residue 480 ILE Chi-restraints excluded: chain I residue 226 MET Chi-restraints excluded: chain I residue 313 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [131, 121, 22, 1, 2, 154, 9, 37, 114, 85, 33] chunk 131 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN E 69 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN I 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.093486 restraints weight = 62567.516| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.99 r_work: 0.2997 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17570 Z= 0.122 Angle : 0.517 9.251 24000 Z= 0.257 Chirality : 0.040 0.185 2705 Planarity : 0.003 0.039 2960 Dihedral : 4.265 30.144 2790 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.14 % Allowed : 9.37 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.18), residues: 2060 helix: 1.76 (0.16), residues: 890 sheet: 0.57 (0.26), residues: 400 loop : -0.25 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.009 0.001 TYR C 442 PHE 0.009 0.001 PHE I 275 TRP 0.008 0.001 TRP E 82 HIS 0.003 0.001 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (17525) covalent geometry : angle 0.49267 / 0.25 (23885) SS BOND : bond 0.00799 / 0.53 ( 20) SS BOND : angle 3.15384 / 2.03 ( 40) hydrogen bonds : bond 0.03608 / 2.34 ( 863) hydrogen bonds : angle 4.39446 / 3.06 ( 2841) link_BETA1-4 : bond 0.00206 / 0.14 ( 10) link_BETA1-4 : angle 1.05724 / 0.71 ( 30) link_NAG-ASN : bond 0.00146 / 0.10 ( 15) link_NAG-ASN : angle 2.01880 / 1.48 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8458 (m110) cc_final: 0.8188 (m110) REVERT: A 341 TRP cc_start: 0.8264 (t60) cc_final: 0.7653 (t60) REVERT: A 342 PHE cc_start: 0.7683 (t80) cc_final: 0.6032 (m-10) REVERT: C 341 TRP cc_start: 0.8304 (t60) cc_final: 0.7938 (t60) REVERT: C 438 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6498 (mm-30) REVERT: E 116 ASN cc_start: 0.8479 (m110) cc_final: 0.8206 (m110) REVERT: E 197 ASP cc_start: 0.8231 (t70) cc_final: 0.7898 (t0) REVERT: E 208 ARG cc_start: 0.7630 (mmt180) cc_final: 0.7006 (mmt-90) REVERT: E 277 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7070 (tp) REVERT: E 288 ASP cc_start: 0.7665 (p0) cc_final: 0.7431 (t0) REVERT: E 342 PHE cc_start: 0.7396 (t80) cc_final: 0.5977 (m-10) REVERT: G 64 ASP cc_start: 0.8158 (t0) cc_final: 0.7888 (t0) REVERT: G 66 ASP cc_start: 0.7785 (t70) cc_final: 0.6778 (t0) REVERT: G 68 LYS cc_start: 0.8691 (tttm) cc_final: 0.8364 (tttp) REVERT: G 69 ASN cc_start: 0.8634 (m110) cc_final: 0.8311 (m-40) REVERT: G 197 ASP cc_start: 0.8486 (t70) cc_final: 0.8184 (t0) REVERT: G 342 PHE cc_start: 0.7533 (t80) cc_final: 0.6163 (m-10) REVERT: I 313 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6663 (mp) REVERT: I 341 TRP cc_start: 0.8415 (t60) cc_final: 0.7935 (t60) outliers start: 21 outliers final: 8 residues processed: 177 average time/residue: 0.5697 time to fit residues: 113.6010 Evaluate side-chains 169 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 476 SER Chi-restraints excluded: chain G residue 226 MET Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain I residue 226 MET Chi-restraints excluded: chain I residue 313 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [197, 103, 122, 128, 19, 92, 135, 171, 121, 37, 48] chunk 197 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 128 optimal weight: 0.7980 chunk 19 optimal weight: 0.0050 chunk 92 optimal weight: 0.4980 chunk 135 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095197 restraints weight = 64044.362| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.06 r_work: 0.3018 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 17570 Z= 0.103 Angle : 0.496 8.334 24000 Z= 0.247 Chirality : 0.039 0.177 2705 Planarity : 0.003 0.039 2960 Dihedral : 3.928 29.842 2790 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.98 % Allowed : 9.86 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.23 (0.18), residues: 2060 helix: 1.84 (0.16), residues: 890 sheet: 0.53 (0.25), residues: 410 loop : -0.17 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.007 0.001 TYR C 442 PHE 0.009 0.001 PHE I 275 TRP 0.007 0.001 TRP E 82 HIS 0.003 0.000 HIS E 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (17525) covalent geometry : angle 0.47263 / 0.24 (23885) SS BOND : bond 0.00775 / 0.52 ( 20) SS BOND : angle 3.05567 / 1.95 ( 40) hydrogen bonds : bond 0.03393 / 2.20 ( 863) hydrogen bonds : angle 4.27382 / 2.98 ( 2841) link_BETA1-4 : bond 0.00280 / 0.19 ( 10) link_BETA1-4 : angle 0.95789 / 0.65 ( 30) link_NAG-ASN : bond 0.00123 / 0.08 ( 15) link_NAG-ASN : angle 1.92467 / 1.41 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8414 (m110) cc_final: 0.8123 (m110) REVERT: A 277 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7040 (tp) REVERT: A 341 TRP cc_start: 0.8330 (t60) cc_final: 0.7663 (t60) REVERT: A 342 PHE cc_start: 0.7695 (t80) cc_final: 0.6003 (m-10) REVERT: C 341 TRP cc_start: 0.8338 (t60) cc_final: 0.7941 (t60) REVERT: C 438 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6570 (mm-30) REVERT: E 116 ASN cc_start: 0.8424 (m110) cc_final: 0.8204 (m110) REVERT: E 197 ASP cc_start: 0.8133 (t70) cc_final: 0.7758 (t0) REVERT: E 208 ARG cc_start: 0.7663 (mmt180) cc_final: 0.7008 (mmt-90) REVERT: E 277 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7041 (tp) REVERT: E 288 ASP cc_start: 0.7667 (p0) cc_final: 0.7449 (t0) REVERT: E 316 GLN cc_start: 0.8087 (tt0) cc_final: 0.7570 (mt0) REVERT: E 342 PHE cc_start: 0.7383 (t80) cc_final: 0.5972 (m-10) REVERT: G 64 ASP cc_start: 0.8129 (t0) cc_final: 0.7886 (t0) REVERT: G 66 ASP cc_start: 0.7797 (t70) cc_final: 0.6755 (t0) REVERT: G 68 LYS cc_start: 0.8707 (tttm) cc_final: 0.8378 (tttp) REVERT: G 69 ASN cc_start: 0.8630 (m110) cc_final: 0.8312 (m-40) REVERT: G 120 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: G 197 ASP cc_start: 0.8468 (t70) cc_final: 0.8192 (t0) REVERT: G 342 PHE cc_start: 0.7531 (t80) cc_final: 0.6158 (m-10) REVERT: I 313 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.6732 (mp) REVERT: I 341 TRP cc_start: 0.8452 (t60) cc_final: 0.7935 (t60) outliers start: 18 outliers final: 10 residues processed: 190 average time/residue: 0.4921 time to fit residues: 106.4561 Evaluate side-chains 182 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 476 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 226 MET Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain G residue 480 ILE Chi-restraints excluded: chain I residue 226 MET Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 468 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [35, 22, 52, 134, 132, 97, 69, 176, 39, 55, 192] chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 137 HIS A ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 ASN I 79 GLN I 139 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.089681 restraints weight = 57975.124| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.83 r_work: 0.2942 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17570 Z= 0.203 Angle : 0.578 8.556 24000 Z= 0.289 Chirality : 0.042 0.192 2705 Planarity : 0.004 0.038 2960 Dihedral : 4.128 29.224 2790 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.31 % Allowed : 10.41 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.05 (0.18), residues: 2060 helix: 1.62 (0.16), residues: 890 sheet: 0.38 (0.25), residues: 430 loop : -0.13 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 229 TYR 0.013 0.001 TYR C 442 PHE 0.012 0.001 PHE C 275 TRP 0.011 0.001 TRP E 330 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (17525) covalent geometry : angle 0.55393 / 0.28 (23885) SS BOND : bond 0.00783 / 0.52 ( 20) SS BOND : angle 3.19848 / 2.04 ( 40) hydrogen bonds : bond 0.04235 / 2.76 ( 863) hydrogen bonds : angle 4.59959 / 3.21 ( 2841) link_BETA1-4 : bond 0.00120 / 0.09 ( 10) link_BETA1-4 : angle 1.18786 / 0.79 ( 30) link_NAG-ASN : bond 0.00329 / 0.22 ( 15) link_NAG-ASN : angle 2.23993 / 1.67 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8493 (m110) cc_final: 0.8250 (m110) REVERT: A 283 MET cc_start: 0.7653 (ttp) cc_final: 0.6836 (ttp) REVERT: A 341 TRP cc_start: 0.8364 (t60) cc_final: 0.7657 (t60) REVERT: A 342 PHE cc_start: 0.7744 (t80) cc_final: 0.6068 (m-10) REVERT: C 281 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7531 (mt-10) REVERT: C 341 TRP cc_start: 0.8340 (t60) cc_final: 0.7905 (t60) REVERT: C 438 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6700 (mm-30) REVERT: E 116 ASN cc_start: 0.8582 (m110) cc_final: 0.8244 (m110) REVERT: E 208 ARG cc_start: 0.7650 (mmt180) cc_final: 0.7037 (mmt-90) REVERT: E 277 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7190 (tp) REVERT: E 281 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7717 (mt-10) REVERT: E 342 PHE cc_start: 0.7446 (t80) cc_final: 0.5960 (m-10) REVERT: F 16 CYS cc_start: 0.6605 (m) cc_final: 0.6200 (m) REVERT: G 64 ASP cc_start: 0.8212 (t0) cc_final: 0.7889 (t0) REVERT: G 66 ASP cc_start: 0.7967 (t70) cc_final: 0.6951 (t0) REVERT: G 68 LYS cc_start: 0.8742 (tttm) cc_final: 0.8414 (tttp) REVERT: G 69 ASN cc_start: 0.8665 (m110) cc_final: 0.8408 (m-40) REVERT: G 342 PHE cc_start: 0.7510 (t80) cc_final: 0.6018 (m-10) REVERT: I 313 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7099 (mt) REVERT: I 341 TRP cc_start: 0.8541 (t60) cc_final: 0.8033 (t60) outliers start: 24 outliers final: 8 residues processed: 186 average time/residue: 0.5967 time to fit residues: 124.3636 Evaluate side-chains 177 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 476 SER Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 468 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [126, 94, 22, 173, 7, 151, 37, 184, 92, 28, 99] chunk 126 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 99 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 ASN I 79 GLN I 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.092409 restraints weight = 57019.245| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.82 r_work: 0.2987 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17570 Z= 0.113 Angle : 0.518 8.528 24000 Z= 0.258 Chirality : 0.040 0.175 2705 Planarity : 0.003 0.040 2960 Dihedral : 3.975 29.288 2790 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.76 % Allowed : 11.28 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.09 (0.18), residues: 2060 helix: 1.70 (0.16), residues: 890 sheet: 0.51 (0.26), residues: 400 loop : -0.23 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 13 TYR 0.009 0.001 TYR C 442 PHE 0.011 0.001 PHE I 275 TRP 0.007 0.001 TRP G 341 HIS 0.002 0.001 HIS E 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (17525) covalent geometry : angle 0.49469 / 0.25 (23885) SS BOND : bond 0.00764 / 0.51 ( 20) SS BOND : angle 3.05137 / 1.94 ( 40) hydrogen bonds : bond 0.03740 / 2.42 ( 863) hydrogen bonds : angle 4.44149 / 3.10 ( 2841) link_BETA1-4 : bond 0.00280 / 0.19 ( 10) link_BETA1-4 : angle 1.02230 / 0.69 ( 30) link_NAG-ASN : bond 0.00130 / 0.09 ( 15) link_NAG-ASN : angle 2.04537 / 1.52 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8480 (m110) cc_final: 0.8230 (m110) REVERT: A 197 ASP cc_start: 0.8528 (t70) cc_final: 0.8256 (t0) REVERT: A 226 MET cc_start: 0.9019 (ptt) cc_final: 0.8761 (ptm) REVERT: A 283 MET cc_start: 0.7634 (ttp) cc_final: 0.6824 (ttp) REVERT: A 341 TRP cc_start: 0.8349 (t60) cc_final: 0.7638 (t60) REVERT: A 342 PHE cc_start: 0.7737 (t80) cc_final: 0.6030 (m-10) REVERT: C 281 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7448 (mt-10) REVERT: C 341 TRP cc_start: 0.8356 (t60) cc_final: 0.7900 (t60) REVERT: C 438 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6655 (mm-30) REVERT: E 116 ASN cc_start: 0.8497 (m110) cc_final: 0.8220 (m110) REVERT: E 197 ASP cc_start: 0.8272 (t70) cc_final: 0.7960 (t0) REVERT: E 208 ARG cc_start: 0.7681 (mmt180) cc_final: 0.6938 (mmt-90) REVERT: E 277 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7105 (tp) REVERT: E 281 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7816 (mt-10) REVERT: E 342 PHE cc_start: 0.7439 (t80) cc_final: 0.5989 (m-10) REVERT: F 16 CYS cc_start: 0.6445 (m) cc_final: 0.6013 (m) REVERT: G 64 ASP cc_start: 0.8144 (t0) cc_final: 0.7833 (t0) REVERT: G 66 ASP cc_start: 0.7939 (t70) cc_final: 0.6889 (t0) REVERT: G 68 LYS cc_start: 0.8699 (tttm) cc_final: 0.8374 (tttp) REVERT: G 69 ASN cc_start: 0.8641 (m110) cc_final: 0.8335 (m-40) REVERT: G 342 PHE cc_start: 0.7488 (t80) cc_final: 0.6004 (m-10) REVERT: I 313 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.6806 (mp) REVERT: I 341 TRP cc_start: 0.8529 (t60) cc_final: 0.7996 (t60) outliers start: 14 outliers final: 7 residues processed: 185 average time/residue: 0.5654 time to fit residues: 117.8281 Evaluate side-chains 175 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 476 SER Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain G residue 480 ILE Chi-restraints excluded: chain I residue 226 MET Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 468 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [158, 13, 46, 98, 112, 30, 145, 87, 168, 9, 59] chunk 158 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 0.0040 chunk 112 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.4910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.094586 restraints weight = 53001.140| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.73 r_work: 0.3019 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 17570 Z= 0.106 Angle : 0.508 8.534 24000 Z= 0.251 Chirality : 0.040 0.181 2705 Planarity : 0.003 0.038 2960 Dihedral : 3.792 29.185 2790 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.76 % Allowed : 11.61 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.18 (0.18), residues: 2060 helix: 1.80 (0.16), residues: 890 sheet: 0.49 (0.25), residues: 410 loop : -0.18 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 42 TYR 0.008 0.001 TYR C 442 PHE 0.010 0.001 PHE I 275 TRP 0.008 0.001 TRP E 82 HIS 0.003 0.000 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (17525) covalent geometry : angle 0.48533 / 0.24 (23885) SS BOND : bond 0.00776 / 0.52 ( 20) SS BOND : angle 3.04338 / 1.93 ( 40) hydrogen bonds : bond 0.03476 / 2.25 ( 863) hydrogen bonds : angle 4.29938 / 3.00 ( 2841) link_BETA1-4 : bond 0.00266 / 0.18 ( 10) link_BETA1-4 : angle 1.06776 / 0.72 ( 30) link_NAG-ASN : bond 0.00102 / 0.07 ( 15) link_NAG-ASN : angle 1.93328 / 1.42 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8424 (m110) cc_final: 0.8193 (m110) REVERT: A 197 ASP cc_start: 0.8467 (t70) cc_final: 0.8264 (t0) REVERT: A 226 MET cc_start: 0.8932 (ptt) cc_final: 0.8686 (ptm) REVERT: A 283 MET cc_start: 0.7630 (ttp) cc_final: 0.6739 (ttp) REVERT: A 341 TRP cc_start: 0.8338 (t60) cc_final: 0.7577 (t60) REVERT: A 342 PHE cc_start: 0.7718 (t80) cc_final: 0.6040 (m-10) REVERT: C 281 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 341 TRP cc_start: 0.8439 (t60) cc_final: 0.7913 (t60) REVERT: C 438 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6631 (mm-30) REVERT: E 116 ASN cc_start: 0.8427 (m110) cc_final: 0.8220 (m110) REVERT: E 197 ASP cc_start: 0.8189 (t70) cc_final: 0.7808 (t0) REVERT: E 208 ARG cc_start: 0.7692 (mmt180) cc_final: 0.7485 (mmt180) REVERT: E 277 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7029 (tp) REVERT: E 342 PHE cc_start: 0.7464 (t80) cc_final: 0.5948 (m-10) REVERT: F 16 CYS cc_start: 0.6384 (m) cc_final: 0.5946 (m) REVERT: G 64 ASP cc_start: 0.8140 (t0) cc_final: 0.7861 (t0) REVERT: G 66 ASP cc_start: 0.7918 (t70) cc_final: 0.6867 (t0) REVERT: G 68 LYS cc_start: 0.8696 (tttm) cc_final: 0.8368 (tttp) REVERT: G 69 ASN cc_start: 0.8635 (m110) cc_final: 0.8330 (m-40) REVERT: G 197 ASP cc_start: 0.8453 (t70) cc_final: 0.8157 (t0) REVERT: G 342 PHE cc_start: 0.7468 (t80) cc_final: 0.5985 (m-10) REVERT: I 313 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.6807 (mp) REVERT: I 341 TRP cc_start: 0.8545 (t60) cc_final: 0.8005 (t60) outliers start: 14 outliers final: 9 residues processed: 186 average time/residue: 0.5411 time to fit residues: 113.5103 Evaluate side-chains 181 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 476 SER Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain G residue 480 ILE Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain I residue 226 MET Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 468 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [29, 133, 22, 186, 126, 94, 168, 74, 163, 53, 80] chunk 29 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093142 restraints weight = 63496.038| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 4.02 r_work: 0.2986 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17570 Z= 0.122 Angle : 0.515 8.569 24000 Z= 0.255 Chirality : 0.040 0.180 2705 Planarity : 0.003 0.038 2960 Dihedral : 3.773 29.059 2790 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.76 % Allowed : 11.93 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.17 (0.18), residues: 2060 helix: 1.77 (0.16), residues: 890 sheet: 0.57 (0.26), residues: 400 loop : -0.22 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 13 TYR 0.009 0.001 TYR C 442 PHE 0.010 0.001 PHE I 275 TRP 0.007 0.001 TRP E 82 HIS 0.003 0.001 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (17525) covalent geometry : angle 0.49217 / 0.25 (23885) SS BOND : bond 0.00765 / 0.51 ( 20) SS BOND : angle 3.06595 / 1.95 ( 40) hydrogen bonds : bond 0.03578 / 2.32 ( 863) hydrogen bonds : angle 4.33372 / 3.03 ( 2841) link_BETA1-4 : bond 0.00237 / 0.16 ( 10) link_BETA1-4 : angle 1.07688 / 0.73 ( 30) link_NAG-ASN : bond 0.00134 / 0.09 ( 15) link_NAG-ASN : angle 1.93507 / 1.42 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8440 (m110) cc_final: 0.8211 (m110) REVERT: A 197 ASP cc_start: 0.8526 (t70) cc_final: 0.8279 (t0) REVERT: A 226 MET cc_start: 0.8979 (ptt) cc_final: 0.8721 (ptm) REVERT: A 283 MET cc_start: 0.7629 (ttp) cc_final: 0.6784 (ttp) REVERT: A 341 TRP cc_start: 0.8415 (t60) cc_final: 0.7683 (t60) REVERT: A 342 PHE cc_start: 0.7712 (t80) cc_final: 0.6024 (m-10) REVERT: C 281 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7431 (mt-10) REVERT: C 341 TRP cc_start: 0.8463 (t60) cc_final: 0.7928 (t60) REVERT: C 438 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6641 (mm-30) REVERT: E 116 ASN cc_start: 0.8463 (m110) cc_final: 0.8221 (m110) REVERT: E 197 ASP cc_start: 0.8232 (t70) cc_final: 0.7898 (t0) REVERT: E 208 ARG cc_start: 0.7718 (mmt180) cc_final: 0.7500 (mmt180) REVERT: E 277 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7063 (tp) REVERT: E 342 PHE cc_start: 0.7444 (t80) cc_final: 0.5906 (m-10) REVERT: F 16 CYS cc_start: 0.6385 (m) cc_final: 0.5947 (m) REVERT: G 64 ASP cc_start: 0.8167 (t0) cc_final: 0.7872 (t0) REVERT: G 66 ASP cc_start: 0.7927 (t70) cc_final: 0.6864 (t0) REVERT: G 68 LYS cc_start: 0.8689 (tttm) cc_final: 0.8356 (tttp) REVERT: G 69 ASN cc_start: 0.8641 (m110) cc_final: 0.8377 (m-40) REVERT: G 197 ASP cc_start: 0.8501 (t70) cc_final: 0.8183 (t0) REVERT: G 342 PHE cc_start: 0.7455 (t80) cc_final: 0.5974 (m-10) REVERT: I 313 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.6828 (mp) REVERT: I 341 TRP cc_start: 0.8586 (t60) cc_final: 0.8025 (t60) outliers start: 14 outliers final: 10 residues processed: 181 average time/residue: 0.5341 time to fit residues: 109.4605 Evaluate side-chains 177 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 476 SER Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain I residue 226 MET Chi-restraints excluded: chain I residue 313 ILE Chi-restraints excluded: chain I residue 468 ASP Chi-restraints excluded: chain I residue 473 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [115, 122, 51, 97, 176, 78, 154, 41, 26, 113, 177] chunk 115 optimal weight: 0.9980 chunk 122 optimal weight: 0.0040 chunk 51 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 176 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 177 optimal weight: 0.0870 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.092899 restraints weight = 74024.674| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 4.29 r_work: 0.2979 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 17570 Z= 0.138 Angle : 0.725 59.175 24000 Z= 0.415 Chirality : 0.041 0.610 2705 Planarity : 0.003 0.038 2960 Dihedral : 3.902 52.835 2790 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.20 % Rotamer: Outliers : 0.71 % Allowed : 11.83 % Favored : 87.47 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 2060 helix: 1.78 (0.16), residues: 890 sheet: 0.57 (0.26), residues: 400 loop : -0.24 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 13 TYR 0.009 0.001 TYR C 442 PHE 0.010 0.001 PHE I 275 TRP 0.007 0.001 TRP A 82 HIS 0.002 0.000 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (17525) covalent geometry : angle 0.70987 / 0.41 (23885) SS BOND : bond 0.00765 / 0.51 ( 20) SS BOND : angle 3.05890 / 1.94 ( 40) hydrogen bonds : bond 0.03552 / 2.30 ( 863) hydrogen bonds : angle 4.33396 / 3.03 ( 2841) link_BETA1-4 : bond 0.00240 / 0.16 ( 10) link_BETA1-4 : angle 1.11671 / 0.76 ( 30) link_NAG-ASN : bond 0.00128 / 0.09 ( 15) link_NAG-ASN : angle 1.93663 / 1.42 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5307.75 seconds wall clock time: 91 minutes 7.58 seconds (5467.58 seconds total)