Starting phenix.real_space_refine on Fri Feb 6 14:54:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wm4_32599/02_2026/7wm4_32599.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm4_32599/02_2026/7wm4_32599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wm4_32599/02_2026/7wm4_32599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm4_32599/02_2026/7wm4_32599.map" model { file = "/net/cci-nas-00/data/ceres_data/7wm4_32599/02_2026/7wm4_32599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm4_32599/02_2026/7wm4_32599.cif" } resolution = 3.2 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= 0.001 sd= 0.017 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: 5 Type Number sf(0) Gaussians P 162 5.49 5 S 56 5.16 5 C 15795 2.51 5 N 4273 2.21 5 O 5562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25848 Number of models: 1 Model: "" Number of chains: 38 Chain: "C" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5310 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 632} Chain breaks: 2 Chain: "D" Number of atoms: 5360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5360 Classifications: {'peptide': 668} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 639} Chain breaks: 1 Chain: "E" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5310 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 632} Chain breaks: 2 Chain: "F" Number of atoms: 5360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5360 Classifications: {'peptide': 668} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 639} Chain breaks: 1 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1702 Classifications: {'RNA': 81} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 39, 'rna3p_pyr': 39} Link IDs: {'rna2p': 3, 'rna3p': 77} Chain: "B" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1700 Classifications: {'RNA': 81} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 39, 'rna3p_pyr': 41} Link IDs: {'rna2p': 1, 'rna3p': 79} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.14, per 1000 atoms: 0.24 Number of scatterers: 25848 At special positions: 0 Unit cell: (223.344, 181.608, 110.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 162 15.00 O 5562 8.00 N 4273 7.00 C 15795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS C 29 " - pdb=" SG CYS C 38 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 650 " - pdb=" SG CYS C 678 " distance=2.03 Simple disulfide: pdb=" SG CYS C 652 " - pdb=" SG CYS C 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 38 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 650 " - pdb=" SG CYS D 678 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 38 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 650 " - pdb=" SG CYS E 678 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 697 " distance=2.03 Simple disulfide: pdb=" SG CYS F 29 " - pdb=" SG CYS F 38 " distance=2.03 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 650 " - pdb=" SG CYS F 678 " distance=2.03 Simple disulfide: pdb=" SG CYS F 652 " - pdb=" SG CYS F 697 " 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=2, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG C 801 " - " ASN C 71 " " NAG C 802 " - " ASN C 197 " " NAG D 801 " - " ASN D 71 " " NAG D 802 " - " ASN D 197 " " NAG D 803 " - " ASN D 276 " " NAG D 804 " - " ASN D 292 " " NAG E 801 " - " ASN E 71 " " NAG E 802 " - " ASN E 197 " " NAG F 801 " - " ASN F 71 " " NAG F 802 " - " ASN F 197 " " NAG F 803 " - " ASN F 276 " " NAG F 804 " - " ASN F 292 " " NAG G 1 " - " ASN C 248 " " NAG H 1 " - " ASN C 253 " " NAG I 1 " - " ASN C 276 " " NAG J 1 " - " ASN C 292 " " NAG K 1 " - " ASN C 399 " " NAG L 1 " - " ASN C 414 " " NAG M 1 " - " ASN C 425 " " NAG N 1 " - " ASN C 508 " " NAG O 1 " - " ASN D 248 " " NAG P 1 " - " ASN D 253 " " NAG Q 1 " - " ASN D 399 " " NAG R 1 " - " ASN D 414 " " NAG S 1 " - " ASN D 425 " " NAG T 1 " - " ASN D 508 " " NAG U 1 " - " ASN E 248 " " NAG V 1 " - " ASN E 253 " " NAG W 1 " - " ASN E 276 " " NAG X 1 " - " ASN E 292 " " NAG Y 1 " - " ASN E 399 " " NAG Z 1 " - " ASN E 414 " " NAG a 1 " - " ASN E 425 " " NAG b 1 " - " ASN E 508 " " NAG c 1 " - " ASN F 248 " " NAG d 1 " - " ASN F 253 " " NAG e 1 " - " ASN F 399 " " NAG f 1 " - " ASN F 414 " " NAG g 1 " - " ASN F 425 " " NAG h 1 " - " ASN F 508 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 799.8 milliseconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5108 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 39 sheets defined 9.9% alpha, 10.3% beta 65 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'C' and resid 93 through 99 removed outlier: 3.580A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.555A pdb=" N THR C 119 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 121 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 269 through 275 removed outlier: 4.197A pdb=" N TRP C 274 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 4.160A pdb=" N HIS C 407 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 454 removed outlier: 3.584A pdb=" N TRP C 453 " --> pdb=" O GLY C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 632 Processing helix chain 'C' and resid 633 through 636 Processing helix chain 'C' and resid 655 through 664 Processing helix chain 'D' and resid 93 through 99 removed outlier: 3.723A pdb=" N GLN D 97 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 235 through 246 removed outlier: 3.699A pdb=" N TRP D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.928A pdb=" N TRP D 274 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 4.430A pdb=" N SER D 404 " --> pdb=" O THR D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 454 Processing helix chain 'D' and resid 627 through 632 removed outlier: 3.536A pdb=" N PHE D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 636 Processing helix chain 'D' and resid 655 through 664 Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 116 through 121 removed outlier: 3.611A pdb=" N THR E 119 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL E 121 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 246 Processing helix chain 'E' and resid 269 through 275 removed outlier: 4.226A pdb=" N TRP E 274 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 406 Processing helix chain 'E' and resid 450 through 454 removed outlier: 3.689A pdb=" N TRP E 453 " --> pdb=" O GLY E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 632 Processing helix chain 'E' and resid 633 through 636 Processing helix chain 'E' and resid 655 through 664 Processing helix chain 'F' and resid 93 through 99 removed outlier: 3.772A pdb=" N GLN F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'F' and resid 235 through 246 removed outlier: 3.643A pdb=" N TRP F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU F 245 " --> pdb=" O LYS F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 removed outlier: 3.985A pdb=" N TRP F 274 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 407 removed outlier: 4.421A pdb=" N SER F 404 " --> pdb=" O THR F 401 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS F 407 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 454 Processing helix chain 'F' and resid 543 through 547 Processing helix chain 'F' and resid 627 through 632 Processing helix chain 'F' and resid 633 through 636 Processing helix chain 'F' and resid 651 through 664 removed outlier: 3.809A pdb=" N SER F 656 " --> pdb=" O CYS F 652 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP F 657 " --> pdb=" O GLU F 653 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHE F 658 " --> pdb=" O SER F 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.837A pdb=" N LEU C 57 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 81 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN C 106 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 129 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 154 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 153 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 177 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 186 through 187 removed outlier: 3.862A pdb=" N LEU C 187 " --> pdb=" O GLU C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 199 through 200 Processing sheet with id=AA4, first strand: chain 'C' and resid 226 through 228 removed outlier: 6.939A pdb=" N LEU C 227 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU C 254 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU C 280 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 462 " --> pdb=" O ARG C 485 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET C 487 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU C 486 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE C 592 " --> pdb=" O ASN C 617 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 616 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AA6, first strand: chain 'C' and resid 313 through 314 removed outlier: 4.053A pdb=" N LEU C 314 " --> pdb=" O ASN C 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 396 through 397 Processing sheet with id=AA8, first strand: chain 'C' and resid 445 through 447 removed outlier: 6.725A pdb=" N GLN C 446 " --> pdb=" O GLN C 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 648 through 649 removed outlier: 7.320A pdb=" N PHE C 648 " --> pdb=" O ASN C 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.800A pdb=" N LEU D 57 " --> pdb=" O ASP D 82 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 106 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 152 through 154 removed outlier: 6.695A pdb=" N LEU D 153 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU D 177 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU D 227 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU D 254 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 187 removed outlier: 3.670A pdb=" N LEU D 187 " --> pdb=" O GLU D 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 199 through 200 Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 264 Processing sheet with id=AB6, first strand: chain 'D' and resid 313 through 314 removed outlier: 4.111A pdb=" N LEU D 314 " --> pdb=" O ASN D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.981A pdb=" N LEU D 413 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AB9, first strand: chain 'D' and resid 445 through 447 removed outlier: 7.530A pdb=" N GLN D 446 " --> pdb=" O GLN D 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 461 through 463 removed outlier: 4.088A pdb=" N MET D 487 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 592 " --> pdb=" O ASN D 617 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 648 through 649 removed outlier: 7.181A pdb=" N PHE D 648 " --> pdb=" O ASN D 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.876A pdb=" N LEU E 57 " --> pdb=" O ASP E 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 104 through 106 removed outlier: 6.747A pdb=" N LEU E 153 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU E 177 " --> pdb=" O ASP E 204 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET E 487 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU E 486 " --> pdb=" O ASP E 513 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP E 537 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE E 592 " --> pdb=" O ASN E 617 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU E 616 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 186 through 187 removed outlier: 3.704A pdb=" N LEU E 187 " --> pdb=" O GLU E 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 199 through 200 Processing sheet with id=AC7, first strand: chain 'E' and resid 263 through 264 Processing sheet with id=AC8, first strand: chain 'E' and resid 313 through 314 removed outlier: 4.206A pdb=" N LEU E 314 " --> pdb=" O ASN E 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 396 through 397 Processing sheet with id=AD1, first strand: chain 'E' and resid 445 through 447 removed outlier: 6.598A pdb=" N GLN E 446 " --> pdb=" O GLN E 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 648 through 649 removed outlier: 7.216A pdb=" N PHE E 648 " --> pdb=" O ASN E 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 35 through 37 removed outlier: 6.548A pdb=" N ALA F 36 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F 57 " --> pdb=" O ASP F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 104 through 106 removed outlier: 6.475A pdb=" N LEU F 153 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU F 177 " --> pdb=" O ASP F 204 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU F 227 " --> pdb=" O SER F 255 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU F 254 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 186 through 187 removed outlier: 3.668A pdb=" N LEU F 187 " --> pdb=" O GLU F 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 199 through 200 Processing sheet with id=AD7, first strand: chain 'F' and resid 263 through 264 Processing sheet with id=AD8, first strand: chain 'F' and resid 313 through 314 removed outlier: 4.154A pdb=" N LEU F 314 " --> pdb=" O ASN F 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'F' and resid 396 through 397 Processing sheet with id=AE1, first strand: chain 'F' and resid 436 through 438 removed outlier: 6.999A pdb=" N LEU F 437 " --> pdb=" O TYR F 463 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET F 487 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU F 536 " --> pdb=" O ASN F 569 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE F 592 " --> pdb=" O ASN F 617 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU F 616 " --> pdb=" O ASP F 642 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 445 through 447 removed outlier: 7.411A pdb=" N GLN F 446 " --> pdb=" O GLN F 471 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU F 470 " --> pdb=" O LYS F 494 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 648 through 649 removed outlier: 7.244A pdb=" N PHE F 648 " --> pdb=" O ASN F 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 221 hydrogen bonds defined for protein. 552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 130 hydrogen bonds 260 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7508 1.34 - 1.46: 5415 1.46 - 1.57: 13380 1.57 - 1.69: 322 1.69 - 1.81: 72 Bond restraints: 26697 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" C1 NAG D 803 " pdb=" O5 NAG D 803 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C1 NAG D 804 " pdb=" O5 NAG D 804 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.27e+00 ... (remaining 26692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 36451 2.37 - 4.74: 458 4.74 - 7.11: 74 7.11 - 9.48: 1 9.48 - 11.86: 5 Bond angle restraints: 36989 Sorted by residual: angle pdb=" CA LEU C 394 " pdb=" CB LEU C 394 " pdb=" CG LEU C 394 " ideal model delta sigma weight residual 116.30 128.16 -11.86 3.50e+00 8.16e-02 1.15e+01 angle pdb=" CA LEU F 543 " pdb=" CB LEU F 543 " pdb=" CG LEU F 543 " ideal model delta sigma weight residual 116.30 127.27 -10.97 3.50e+00 8.16e-02 9.82e+00 angle pdb=" CA LEU D 394 " pdb=" CB LEU D 394 " pdb=" CG LEU D 394 " ideal model delta sigma weight residual 116.30 126.98 -10.68 3.50e+00 8.16e-02 9.32e+00 angle pdb=" C ASN C 285 " pdb=" N ASN C 286 " pdb=" CA ASN C 286 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.78e+00 angle pdb=" C ASN E 285 " pdb=" N ASN E 286 " pdb=" CA ASN E 286 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.61e+00 ... (remaining 36984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 16467 35.45 - 70.90: 495 70.90 - 106.35: 168 106.35 - 141.79: 24 141.79 - 177.24: 8 Dihedral angle restraints: 17162 sinusoidal: 9338 harmonic: 7824 Sorted by residual: dihedral pdb=" CB CYS F 652 " pdb=" SG CYS F 652 " pdb=" SG CYS F 697 " pdb=" CB CYS F 697 " ideal model delta sinusoidal sigma weight residual -86.00 -175.22 89.22 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS E 96 " pdb=" SG CYS E 96 " pdb=" SG CYS E 123 " pdb=" CB CYS E 123 " ideal model delta sinusoidal sigma weight residual -86.00 -142.57 56.57 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS E 652 " pdb=" SG CYS E 652 " pdb=" SG CYS E 697 " pdb=" CB CYS E 697 " ideal model delta sinusoidal sigma weight residual 93.00 52.41 40.59 1 1.00e+01 1.00e-02 2.31e+01 ... (remaining 17159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4169 0.063 - 0.126: 413 0.126 - 0.190: 39 0.190 - 0.253: 13 0.253 - 0.316: 16 Chirality restraints: 4650 Sorted by residual: chirality pdb=" C1 NAG F 802 " pdb=" ND2 ASN F 197 " pdb=" C2 NAG F 802 " pdb=" O5 NAG F 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C5 BMA g 3 " pdb=" C4 BMA g 3 " pdb=" C6 BMA g 3 " pdb=" O5 BMA g 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 4647 not shown) Planarity restraints: 4058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 50 " -0.039 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO C 51 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 508 " -0.019 2.00e-02 2.50e+03 1.80e-02 4.06e+00 pdb=" CG ASN D 508 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 508 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 508 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 399 " -0.017 2.00e-02 2.50e+03 1.58e-02 3.12e+00 pdb=" CG ASN C 399 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN C 399 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 399 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " -0.015 2.00e-02 2.50e+03 ... (remaining 4055 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 979 2.69 - 3.24: 24782 3.24 - 3.80: 43779 3.80 - 4.35: 56779 4.35 - 4.90: 88672 Nonbonded interactions: 214991 Sorted by model distance: nonbonded pdb=" OG SER D 247 " pdb=" O GLY D 271 " model vdw 2.140 3.040 nonbonded pdb=" O LEU C 171 " pdb=" OG SER C 198 " model vdw 2.181 3.040 nonbonded pdb=" O LEU C 246 " pdb=" OG1 THR C 249 " model vdw 2.201 3.040 nonbonded pdb=" OG SER C 113 " pdb=" O2' U B 50 " model vdw 2.214 3.040 nonbonded pdb=" O4 U A 80 " pdb=" N1 A B 11 " model vdw 2.216 3.120 ... (remaining 214986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 44 or resid 46 through 85)) selection = (chain 'B' and (resid 6 through 45 or resid 47 through 86)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 29 through 336 or resid 343 through 802)) selection = chain 'E' selection = (chain 'F' and (resid 29 through 336 or resid 343 through 802)) } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.100 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26797 Z= 0.168 Angle : 0.673 22.070 37267 Z= 0.291 Chirality : 0.045 0.316 4650 Planarity : 0.003 0.060 4018 Dihedral : 19.005 177.243 12006 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 0.08 % Allowed : 0.36 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.73 (0.16), residues: 2638 helix: -1.05 (0.38), residues: 208 sheet: -1.72 (0.26), residues: 430 loop : -1.07 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 507 TYR 0.008 0.000 TYR F 469 PHE 0.012 0.001 PHE C 503 TRP 0.014 0.001 TRP F 274 HIS 0.004 0.000 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00334 (26697) covalent geometry : angle 0.63041 (36989) SS BOND : bond 0.00111 ( 16) SS BOND : angle 0.35841 ( 32) hydrogen bonds : bond 0.22020 ( 351) hydrogen bonds : angle 7.11394 ( 812) Misc. bond : bond 0.00270 ( 2) link_BETA1-4 : bond 0.00677 ( 42) link_BETA1-4 : angle 2.03650 ( 126) link_NAG-ASN : bond 0.00614 ( 40) link_NAG-ASN : angle 3.71859 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.960 Fit side-chains REVERT: D 144 PHE cc_start: 0.8784 (m-80) cc_final: 0.8513 (m-80) REVERT: D 274 TRP cc_start: 0.8460 (m-90) cc_final: 0.8233 (m-90) REVERT: D 395 GLN cc_start: 0.8696 (mm-40) cc_final: 0.7888 (mm-40) REVERT: D 436 ILE cc_start: 0.3816 (mm) cc_final: 0.3566 (mm) REVERT: E 445 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7625 (tm-30) REVERT: E 488 LEU cc_start: 0.6964 (mm) cc_final: 0.6762 (mt) REVERT: F 120 PHE cc_start: 0.9265 (m-80) cc_final: 0.9033 (m-10) REVERT: F 627 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8149 (mm-30) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.1406 time to fit residues: 36.4726 Evaluate side-chains 110 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN C 433 GLN C 446 GLN C 471 GLN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 ASN D 467 ASN ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 GLN E 467 ASN ** E 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 542 ASN ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 GLN F 467 ASN ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.075173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.061416 restraints weight = 206663.379| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 6.23 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26797 Z= 0.210 Angle : 0.766 20.163 37267 Z= 0.352 Chirality : 0.046 0.350 4650 Planarity : 0.004 0.064 4018 Dihedral : 15.789 168.013 6760 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.14 % Favored : 93.71 % Rotamer: Outliers : 0.96 % Allowed : 8.76 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.92 (0.16), residues: 2638 helix: -1.09 (0.37), residues: 202 sheet: -1.69 (0.26), residues: 424 loop : -1.27 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 489 TYR 0.019 0.002 TYR E 466 PHE 0.018 0.002 PHE E 428 TRP 0.024 0.002 TRP F 274 HIS 0.011 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00449 (26697) covalent geometry : angle 0.72577 (36989) SS BOND : bond 0.00329 ( 16) SS BOND : angle 0.63260 ( 32) hydrogen bonds : bond 0.07031 ( 351) hydrogen bonds : angle 5.24734 ( 812) Misc. bond : bond 0.00184 ( 2) link_BETA1-4 : bond 0.00824 ( 42) link_BETA1-4 : angle 2.43435 ( 126) link_NAG-ASN : bond 0.00836 ( 40) link_NAG-ASN : angle 3.66931 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.674 Fit side-chains REVERT: D 144 PHE cc_start: 0.9218 (m-80) cc_final: 0.8787 (m-80) REVERT: D 274 TRP cc_start: 0.8743 (m-90) cc_final: 0.8426 (m-90) REVERT: D 558 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.6378 (t80) REVERT: E 112 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8553 (mm) REVERT: E 445 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7941 (pp20) REVERT: F 120 PHE cc_start: 0.9526 (m-80) cc_final: 0.9265 (m-10) REVERT: F 558 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6696 (t80) REVERT: F 627 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8437 (mm-30) outliers start: 24 outliers final: 15 residues processed: 118 average time/residue: 0.1204 time to fit residues: 25.7493 Evaluate side-chains 106 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 430 TRP Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 430 TRP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 558 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 226 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 222 optimal weight: 30.0000 chunk 255 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 138 optimal weight: 0.0980 chunk 247 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 367 ASN C 446 GLN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 HIS ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN E 367 ASN E 419 HIS ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 HIS ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 ASN ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.064663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.050964 restraints weight = 215500.630| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 5.93 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26797 Z= 0.242 Angle : 0.787 19.587 37267 Z= 0.376 Chirality : 0.046 0.341 4650 Planarity : 0.005 0.062 4018 Dihedral : 15.740 177.513 6760 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.00 % Favored : 91.89 % Rotamer: Outliers : 1.77 % Allowed : 12.18 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2638 helix: -1.01 (0.38), residues: 188 sheet: -1.86 (0.26), residues: 422 loop : -1.52 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 507 TYR 0.022 0.002 TYR C 360 PHE 0.030 0.002 PHE E 558 TRP 0.017 0.002 TRP E 274 HIS 0.013 0.002 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00513 (26697) covalent geometry : angle 0.75045 (36989) SS BOND : bond 0.00427 ( 16) SS BOND : angle 0.72639 ( 32) hydrogen bonds : bond 0.07635 ( 351) hydrogen bonds : angle 5.19093 ( 812) Misc. bond : bond 0.00049 ( 2) link_BETA1-4 : bond 0.00712 ( 42) link_BETA1-4 : angle 1.95945 ( 126) link_NAG-ASN : bond 0.00741 ( 40) link_NAG-ASN : angle 3.80743 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: C 187 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9176 (tp) REVERT: D 144 PHE cc_start: 0.9282 (m-80) cc_final: 0.8860 (m-80) REVERT: D 274 TRP cc_start: 0.8696 (m-90) cc_final: 0.8367 (m-90) REVERT: D 463 TYR cc_start: 0.7415 (m-10) cc_final: 0.6913 (m-10) REVERT: D 487 MET cc_start: 0.7233 (pmm) cc_final: 0.6936 (pmm) REVERT: E 112 LEU cc_start: 0.8828 (mm) cc_final: 0.8600 (mm) REVERT: E 445 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8070 (pp20) REVERT: F 120 PHE cc_start: 0.9699 (m-80) cc_final: 0.9450 (m-10) REVERT: F 627 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8529 (mm-30) outliers start: 44 outliers final: 21 residues processed: 130 average time/residue: 0.1448 time to fit residues: 33.8292 Evaluate side-chains 101 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 430 TRP Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 430 TRP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 272 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 201 optimal weight: 30.0000 chunk 249 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 170 GLN E 310 ASN ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.065081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.051518 restraints weight = 214060.705| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 5.89 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26797 Z= 0.170 Angle : 0.678 20.843 37267 Z= 0.320 Chirality : 0.043 0.344 4650 Planarity : 0.004 0.060 4018 Dihedral : 15.449 171.852 6760 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.63 % Favored : 93.21 % Rotamer: Outliers : 2.41 % Allowed : 13.67 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2638 helix: -1.03 (0.38), residues: 188 sheet: -2.06 (0.24), residues: 458 loop : -1.45 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 201 TYR 0.012 0.001 TYR C 360 PHE 0.016 0.001 PHE E 558 TRP 0.011 0.001 TRP F 274 HIS 0.005 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00367 (26697) covalent geometry : angle 0.63835 (36989) SS BOND : bond 0.00302 ( 16) SS BOND : angle 0.61255 ( 32) hydrogen bonds : bond 0.05729 ( 351) hydrogen bonds : angle 4.86787 ( 812) Misc. bond : bond 0.00104 ( 2) link_BETA1-4 : bond 0.00624 ( 42) link_BETA1-4 : angle 2.01706 ( 126) link_NAG-ASN : bond 0.00667 ( 40) link_NAG-ASN : angle 3.59812 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 88 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: C 176 GLU cc_start: 0.6620 (mp0) cc_final: 0.6376 (mp0) REVERT: C 187 LEU cc_start: 0.9451 (tp) cc_final: 0.9246 (tp) REVERT: C 335 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8167 (p) REVERT: C 480 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8750 (m) REVERT: C 538 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7779 (m-10) REVERT: D 144 PHE cc_start: 0.9263 (m-80) cc_final: 0.8774 (m-80) REVERT: D 274 TRP cc_start: 0.8642 (m-90) cc_final: 0.8299 (m-90) REVERT: D 463 TYR cc_start: 0.7155 (m-10) cc_final: 0.6814 (m-10) REVERT: E 445 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7970 (pp20) REVERT: E 538 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: F 120 PHE cc_start: 0.9668 (m-80) cc_final: 0.9411 (m-10) outliers start: 60 outliers final: 30 residues processed: 137 average time/residue: 0.1436 time to fit residues: 35.1802 Evaluate side-chains 120 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 430 TRP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 430 TRP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 72 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 47 optimal weight: 0.0980 chunk 117 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 50.0000 chunk 81 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 208 optimal weight: 30.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 495 ASN ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 593 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 = 0.4431 r_free = 0.4431 target = 0.065148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.051459 restraints weight = 210363.167| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 5.85 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26797 Z= 0.141 Angle : 0.645 20.739 37267 Z= 0.305 Chirality : 0.042 0.347 4650 Planarity : 0.003 0.059 4018 Dihedral : 15.343 174.537 6760 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.28 % Favored : 92.57 % Rotamer: Outliers : 2.09 % Allowed : 14.83 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2638 helix: -1.00 (0.38), residues: 188 sheet: -2.13 (0.24), residues: 448 loop : -1.43 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 507 TYR 0.008 0.001 TYR C 360 PHE 0.015 0.001 PHE E 558 TRP 0.009 0.001 TRP E 274 HIS 0.005 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00306 (26697) covalent geometry : angle 0.60588 (36989) SS BOND : bond 0.00242 ( 16) SS BOND : angle 0.54638 ( 32) hydrogen bonds : bond 0.05015 ( 351) hydrogen bonds : angle 4.74069 ( 812) Misc. bond : bond 0.00108 ( 2) link_BETA1-4 : bond 0.00639 ( 42) link_BETA1-4 : angle 1.88510 ( 126) link_NAG-ASN : bond 0.00622 ( 40) link_NAG-ASN : angle 3.50466 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 93 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 187 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9222 (tp) REVERT: C 335 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8151 (p) REVERT: C 480 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8805 (m) REVERT: C 538 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7609 (m-10) REVERT: D 144 PHE cc_start: 0.9238 (m-80) cc_final: 0.8772 (m-80) REVERT: D 274 TRP cc_start: 0.8586 (m-90) cc_final: 0.8254 (m-90) REVERT: D 463 TYR cc_start: 0.7055 (m-10) cc_final: 0.6745 (m-10) REVERT: D 487 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6267 (pmm) REVERT: E 445 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7998 (pp20) REVERT: E 538 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: F 120 PHE cc_start: 0.9618 (m-80) cc_final: 0.9358 (m-10) outliers start: 52 outliers final: 28 residues processed: 130 average time/residue: 0.1394 time to fit residues: 32.6138 Evaluate side-chains 120 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 430 TRP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 430 TRP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 498 ILE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 558 PHE Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 69 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 273 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 ASN C 664 GLN D 58 ASN D 157 HIS ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN E 664 GLN F 58 ASN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.060551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.047427 restraints weight = 220128.410| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 5.70 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 26797 Z= 0.334 Angle : 0.891 20.588 37267 Z= 0.421 Chirality : 0.048 0.349 4650 Planarity : 0.005 0.062 4018 Dihedral : 15.873 175.158 6760 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.84 % Favored : 89.01 % Rotamer: Outliers : 3.01 % Allowed : 15.72 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.15), residues: 2638 helix: -1.28 (0.37), residues: 188 sheet: -2.30 (0.24), residues: 450 loop : -1.79 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 507 TYR 0.016 0.002 TYR C 360 PHE 0.038 0.002 PHE E 558 TRP 0.016 0.002 TRP E 274 HIS 0.009 0.002 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00714 (26697) covalent geometry : angle 0.85727 (36989) SS BOND : bond 0.00554 ( 16) SS BOND : angle 1.03032 ( 32) hydrogen bonds : bond 0.09660 ( 351) hydrogen bonds : angle 5.22529 ( 812) Misc. bond : bond 0.00119 ( 2) link_BETA1-4 : bond 0.00682 ( 42) link_BETA1-4 : angle 2.10070 ( 126) link_NAG-ASN : bond 0.01044 ( 40) link_NAG-ASN : angle 3.88798 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 80 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 LEU cc_start: 0.9331 (tp) cc_final: 0.9020 (tp) REVERT: C 239 THR cc_start: 0.8763 (m) cc_final: 0.8469 (p) REVERT: C 335 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8185 (p) REVERT: C 538 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7391 (m-10) REVERT: D 144 PHE cc_start: 0.9337 (m-80) cc_final: 0.8886 (m-80) REVERT: D 274 TRP cc_start: 0.8727 (m-90) cc_final: 0.8373 (m-90) REVERT: E 538 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: F 120 PHE cc_start: 0.9712 (m-80) cc_final: 0.9449 (m-10) REVERT: F 461 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7353 (pp20) outliers start: 75 outliers final: 44 residues processed: 142 average time/residue: 0.1439 time to fit residues: 36.3042 Evaluate side-chains 119 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 71 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 461 GLU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 558 PHE Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 76 optimal weight: 20.0000 chunk 185 optimal weight: 0.9990 chunk 112 optimal weight: 0.2980 chunk 87 optimal weight: 40.0000 chunk 241 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN ** C 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN F 367 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.077437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.063612 restraints weight = 211052.056| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 5.92 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26797 Z= 0.126 Angle : 0.673 20.826 37267 Z= 0.319 Chirality : 0.043 0.351 4650 Planarity : 0.004 0.058 4018 Dihedral : 15.481 174.063 6760 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.33 % Favored : 93.52 % Rotamer: Outliers : 2.41 % Allowed : 16.64 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.16), residues: 2638 helix: -1.12 (0.37), residues: 188 sheet: -2.30 (0.23), residues: 476 loop : -1.49 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 545 TYR 0.021 0.001 TYR D 463 PHE 0.013 0.001 PHE C 558 TRP 0.014 0.001 TRP D 430 HIS 0.005 0.001 HIS F 540 Details of bonding type rmsd covalent geometry : bond 0.00274 (26697) covalent geometry : angle 0.63532 (36989) SS BOND : bond 0.00242 ( 16) SS BOND : angle 0.66344 ( 32) hydrogen bonds : bond 0.04810 ( 351) hydrogen bonds : angle 4.78947 ( 812) Misc. bond : bond 0.00083 ( 2) link_BETA1-4 : bond 0.00591 ( 42) link_BETA1-4 : angle 1.84117 ( 126) link_NAG-ASN : bond 0.00635 ( 40) link_NAG-ASN : angle 3.52167 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 91 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 187 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9059 (tp) REVERT: C 335 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8099 (p) REVERT: C 381 SER cc_start: 0.7744 (m) cc_final: 0.7537 (t) REVERT: C 538 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: D 144 PHE cc_start: 0.9397 (m-80) cc_final: 0.8900 (m-80) REVERT: D 274 TRP cc_start: 0.8678 (m-90) cc_final: 0.8336 (m-90) REVERT: D 463 TYR cc_start: 0.6912 (m-10) cc_final: 0.6705 (m-10) REVERT: D 558 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.6537 (t80) REVERT: E 538 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: F 120 PHE cc_start: 0.9686 (m-80) cc_final: 0.9434 (m-10) outliers start: 60 outliers final: 39 residues processed: 139 average time/residue: 0.1465 time to fit residues: 35.9571 Evaluate side-chains 126 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 498 ILE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 558 PHE Chi-restraints excluded: chain F residue 598 ASN Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 164 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 226 optimal weight: 0.0270 chunk 131 optimal weight: 10.0000 chunk 146 optimal weight: 0.0040 chunk 144 optimal weight: 8.9990 overall best weight: 1.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 585 ASN ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN E 310 ASN ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.064722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.051140 restraints weight = 211817.221| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 5.98 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 26797 Z= 0.112 Angle : 0.651 20.702 37267 Z= 0.306 Chirality : 0.042 0.349 4650 Planarity : 0.004 0.058 4018 Dihedral : 15.251 175.503 6760 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.67 % Favored : 93.21 % Rotamer: Outliers : 2.21 % Allowed : 17.00 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.16), residues: 2638 helix: -0.53 (0.42), residues: 160 sheet: -2.19 (0.23), residues: 476 loop : -1.38 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 545 TYR 0.014 0.001 TYR D 463 PHE 0.012 0.001 PHE D 503 TRP 0.012 0.001 TRP C 453 HIS 0.014 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00243 (26697) covalent geometry : angle 0.61377 (36989) SS BOND : bond 0.00178 ( 16) SS BOND : angle 0.52127 ( 32) hydrogen bonds : bond 0.04307 ( 351) hydrogen bonds : angle 4.66527 ( 812) Misc. bond : bond 0.00081 ( 2) link_BETA1-4 : bond 0.00566 ( 42) link_BETA1-4 : angle 1.82106 ( 126) link_NAG-ASN : bond 0.00603 ( 40) link_NAG-ASN : angle 3.43121 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 87 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 187 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9088 (tp) REVERT: C 335 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8009 (p) REVERT: C 538 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7415 (m-10) REVERT: D 144 PHE cc_start: 0.9354 (m-80) cc_final: 0.8848 (m-80) REVERT: D 274 TRP cc_start: 0.8584 (m-90) cc_final: 0.8234 (m-90) REVERT: D 558 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.6737 (t80) REVERT: E 538 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7471 (m-10) REVERT: F 120 PHE cc_start: 0.9650 (m-80) cc_final: 0.9395 (m-10) outliers start: 55 outliers final: 36 residues processed: 133 average time/residue: 0.1431 time to fit residues: 33.9335 Evaluate side-chains 124 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain D residue 598 ASN Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 498 ILE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 558 PHE Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 232 optimal weight: 0.8980 chunk 137 optimal weight: 0.3980 chunk 119 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.064049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.050599 restraints weight = 213608.308| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 5.90 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26797 Z= 0.133 Angle : 0.654 20.664 37267 Z= 0.308 Chirality : 0.042 0.348 4650 Planarity : 0.004 0.058 4018 Dihedral : 15.188 176.462 6760 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.28 % Favored : 92.61 % Rotamer: Outliers : 1.97 % Allowed : 17.68 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.16), residues: 2638 helix: -0.51 (0.42), residues: 160 sheet: -2.31 (0.25), residues: 398 loop : -1.46 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 545 TYR 0.040 0.001 TYR D 463 PHE 0.011 0.001 PHE E 558 TRP 0.010 0.001 TRP F 430 HIS 0.016 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00289 (26697) covalent geometry : angle 0.61697 (36989) SS BOND : bond 0.00235 ( 16) SS BOND : angle 0.51978 ( 32) hydrogen bonds : bond 0.04714 ( 351) hydrogen bonds : angle 4.64321 ( 812) Misc. bond : bond 0.00074 ( 2) link_BETA1-4 : bond 0.00551 ( 42) link_BETA1-4 : angle 1.80252 ( 126) link_NAG-ASN : bond 0.00619 ( 40) link_NAG-ASN : angle 3.44052 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 81 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9073 (tp) REVERT: C 335 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8107 (p) REVERT: C 537 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5996 (t0) REVERT: C 538 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7467 (m-10) REVERT: D 144 PHE cc_start: 0.9346 (m-80) cc_final: 0.8831 (m-80) REVERT: D 274 TRP cc_start: 0.8608 (m-90) cc_final: 0.8257 (m-90) REVERT: D 558 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6478 (t80) REVERT: E 538 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7484 (m-10) REVERT: F 120 PHE cc_start: 0.9649 (m-80) cc_final: 0.9383 (m-10) outliers start: 49 outliers final: 36 residues processed: 121 average time/residue: 0.1417 time to fit residues: 30.5979 Evaluate side-chains 120 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 78 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain D residue 598 ASN Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 558 PHE Chi-restraints excluded: chain F residue 598 ASN Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 258 optimal weight: 1.9990 chunk 260 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 206 optimal weight: 40.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 ASN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 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 = 0.4308 r_free = 0.4308 target = 0.061977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.048956 restraints weight = 216242.274| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 5.62 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26797 Z= 0.179 Angle : 0.699 20.602 37267 Z= 0.330 Chirality : 0.043 0.342 4650 Planarity : 0.004 0.059 4018 Dihedral : 15.322 177.120 6760 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.95 % Favored : 90.94 % Rotamer: Outliers : 1.93 % Allowed : 17.64 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.16), residues: 2638 helix: -0.89 (0.40), residues: 176 sheet: -2.31 (0.26), residues: 388 loop : -1.56 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 545 TYR 0.033 0.001 TYR D 463 PHE 0.017 0.001 PHE E 558 TRP 0.012 0.001 TRP E 274 HIS 0.014 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00386 (26697) covalent geometry : angle 0.66415 (36989) SS BOND : bond 0.00315 ( 16) SS BOND : angle 0.64030 ( 32) hydrogen bonds : bond 0.05813 ( 351) hydrogen bonds : angle 4.77354 ( 812) Misc. bond : bond 0.00085 ( 2) link_BETA1-4 : bond 0.00545 ( 42) link_BETA1-4 : angle 1.81736 ( 126) link_NAG-ASN : bond 0.00693 ( 40) link_NAG-ASN : angle 3.51744 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 78 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9046 (tp) REVERT: C 335 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8051 (p) REVERT: C 480 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8731 (m) REVERT: C 538 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7293 (m-10) REVERT: D 144 PHE cc_start: 0.9322 (m-80) cc_final: 0.8818 (m-80) REVERT: D 274 TRP cc_start: 0.8606 (m-90) cc_final: 0.8250 (m-90) REVERT: D 558 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6654 (t80) REVERT: E 538 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7446 (m-10) REVERT: F 120 PHE cc_start: 0.9643 (m-80) cc_final: 0.9351 (m-10) outliers start: 48 outliers final: 37 residues processed: 119 average time/residue: 0.1539 time to fit residues: 32.0055 Evaluate side-chains 120 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain D residue 598 ASN Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 558 PHE Chi-restraints excluded: chain F residue 598 ASN Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 130 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 211 optimal weight: 0.5980 chunk 263 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 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 = 0.4310 r_free = 0.4310 target = 0.061853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.048819 restraints weight = 215389.320| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 5.63 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 26797 Z= 0.213 Angle : 0.815 59.199 37267 Z= 0.419 Chirality : 0.043 0.342 4650 Planarity : 0.004 0.059 4018 Dihedral : 15.328 177.087 6760 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.02 % Favored : 90.86 % Rotamer: Outliers : 1.81 % Allowed : 17.77 % Favored : 80.43 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.16), residues: 2638 helix: -0.89 (0.40), residues: 176 sheet: -2.34 (0.26), residues: 388 loop : -1.57 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 545 TYR 0.026 0.001 TYR D 463 PHE 0.017 0.001 PHE E 558 TRP 0.011 0.001 TRP E 274 HIS 0.013 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00437 (26697) covalent geometry : angle 0.78603 (36989) SS BOND : bond 0.00321 ( 16) SS BOND : angle 0.62350 ( 32) hydrogen bonds : bond 0.05833 ( 351) hydrogen bonds : angle 4.77237 ( 812) Misc. bond : bond 0.00068 ( 2) link_BETA1-4 : bond 0.00514 ( 42) link_BETA1-4 : angle 1.83499 ( 126) link_NAG-ASN : bond 0.00694 ( 40) link_NAG-ASN : angle 3.51852 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6930.26 seconds wall clock time: 120 minutes 11.84 seconds (7211.84 seconds total)