Starting phenix.real_space_refine on Mon Sep 14 07:29:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pz8_20527/09_2026/6pz8_20527.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pz8_20527/09_2026/6pz8_20527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6pz8_20527/09_2026/6pz8_20527.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pz8_20527/09_2026/6pz8_20527.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pz8_20527/09_2026/6pz8_20527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pz8_20527/09_2026/6pz8_20527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pz8_20527/09_2026/6pz8_20527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pz8_20527/09_2026/6pz8_20527.map" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 18096 2.51 5 N 4677 2.21 5 O 5766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28683 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3546 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Chain: "B" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 771 Classifications: {'peptide': 103} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "E" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3546 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Chain: "J" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "C" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "G" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 771 Classifications: {'peptide': 103} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "I" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3546 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Chain: "F" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "D" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "K" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 771 Classifications: {'peptide': 103} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "U" 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 chiralities: 2 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 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 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 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 chiralities: 3 Chain: "Z" 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 chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 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 chiralities: 2 Chain: "f" 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 chiralities: 2 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 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 chiralities: 2 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.25, per 1000 atoms: 0.22 Number of scatterers: 28683 At special positions: 0 Unit cell: (173.4, 186.66, 185.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5766 8.00 N 4677 7.00 C 18096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=1.76 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.04 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.08 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 806 " - pdb=" SG CYS E 828 " distance=2.02 Simple disulfide: pdb=" SG CYS E 811 " - pdb=" SG CYS E 817 " distance=1.76 Simple disulfide: pdb=" SG CYS E 912 " - pdb=" SG CYS E 925 " distance=2.03 Simple disulfide: pdb=" SG CYS E1156 " - pdb=" SG CYS E1164 " distance=2.04 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.04 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.03 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.08 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.03 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.04 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS I 806 " - pdb=" SG CYS I 828 " distance=2.02 Simple disulfide: pdb=" SG CYS I 811 " - pdb=" SG CYS I 817 " distance=1.76 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.03 Simple disulfide: pdb=" SG CYS I1156 " - pdb=" SG CYS I1164 " distance=2.04 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 176 " - pdb=" SG CYS F 214 " distance=2.04 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 339 " - pdb=" SG CYS F 349 " distance=2.03 Simple disulfide: pdb=" SG CYS F 603 " - pdb=" SG CYS F 654 " distance=2.08 Simple disulfide: pdb=" SG CYS F 620 " - pdb=" SG CYS F 650 " distance=2.03 Simple disulfide: pdb=" SG CYS F 679 " - pdb=" SG CYS F 713 " distance=2.04 Simple disulfide: pdb=" SG CYS F 727 " - pdb=" SG CYS F 736 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA a 3 " - " MAN a 5 " " BMA i 3 " - " MAN i 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " 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 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 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 f 1 " - " NAG f 2 " " 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 i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1401 " - " ASN A 774 " " NAG B 801 " - " ASN B 719 " " NAG B 802 " - " ASN B 619 " " NAG B 803 " - " ASN B 66 " " NAG B 807 " - " ASN B 155 " " NAG B 817 " - " ASN B 244 " " NAG E1401 " - " ASN E 774 " " NAG F 801 " - " ASN F 719 " " NAG F 802 " - " ASN F 619 " " NAG F 803 " - " ASN F 66 " " NAG F 807 " - " ASN F 155 " " NAG F 817 " - " ASN F 244 " " NAG I1401 " - " ASN I 774 " " NAG J 801 " - " ASN J 719 " " NAG J 802 " - " ASN J 619 " " NAG J 803 " - " ASN J 66 " " NAG J 807 " - " ASN J 155 " " NAG J 817 " - " ASN J 244 " " NAG M 1 " - " ASN A 785 " " NAG N 1 " - " ASN A1176 " " NAG O 1 " - " ASN A 870 " " NAG P 1 " - " ASN A1213 " " NAG Q 1 " - " ASN B 125 " " NAG R 1 " - " ASN B 166 " " NAG S 1 " - " ASN B 222 " " NAG T 1 " - " ASN B 236 " " NAG U 1 " - " ASN E 785 " " NAG V 1 " - " ASN E1176 " " NAG W 1 " - " ASN E 870 " " NAG X 1 " - " ASN E1213 " " NAG Y 1 " - " ASN J 125 " " NAG Z 1 " - " ASN J 166 " " NAG a 1 " - " ASN J 222 " " NAG b 1 " - " ASN J 236 " " NAG c 1 " - " ASN I 785 " " NAG d 1 " - " ASN I1176 " " NAG e 1 " - " ASN I 870 " " NAG f 1 " - " ASN I1213 " " NAG g 1 " - " ASN F 125 " " NAG h 1 " - " ASN F 166 " " NAG i 1 " - " ASN F 222 " " NAG j 1 " - " ASN F 236 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6612 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 69 sheets defined 24.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 805 through 811 removed outlier: 3.847A pdb=" N CYS A 811 " --> pdb=" O LYS A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.886A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 908 through 913 removed outlier: 3.531A pdb=" N MET A 913 " --> pdb=" O ASP A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 939 through 953 removed outlier: 4.040A pdb=" N MET A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 1007 removed outlier: 5.728A pdb=" N LYS A 995 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU A 996 " --> pdb=" O GLU A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1012 removed outlier: 3.989A pdb=" N PHE A1012 " --> pdb=" O MET A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1039 Processing helix chain 'A' and resid 1040 through 1042 No H-bonds generated for 'chain 'A' and resid 1040 through 1042' Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 4.885A pdb=" N ALA A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.869A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 675 through 682 removed outlier: 6.699A pdb=" N CYS B 679 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU B 680 " --> pdb=" O VAL B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 702 removed outlier: 5.047A pdb=" N ARG B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'E' and resid 805 through 811 removed outlier: 3.847A pdb=" N CYS E 811 " --> pdb=" O LYS E 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 822 Processing helix chain 'E' and resid 824 through 854 removed outlier: 3.886A pdb=" N CYS E 828 " --> pdb=" O TYR E 824 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 852 " --> pdb=" O ASN E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 898 Processing helix chain 'E' and resid 908 through 913 removed outlier: 3.531A pdb=" N MET E 913 " --> pdb=" O ASP E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 931 Processing helix chain 'E' and resid 939 through 953 removed outlier: 4.041A pdb=" N MET E 943 " --> pdb=" O MET E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 971 through 982 Processing helix chain 'E' and resid 986 through 1007 removed outlier: 5.728A pdb=" N LYS E 995 " --> pdb=" O SER E 991 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU E 996 " --> pdb=" O GLU E 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 1007 through 1012 removed outlier: 3.990A pdb=" N PHE E1012 " --> pdb=" O MET E1008 " (cutoff:3.500A) Processing helix chain 'E' and resid 1016 through 1039 Processing helix chain 'E' and resid 1040 through 1042 No H-bonds generated for 'chain 'E' and resid 1040 through 1042' Processing helix chain 'E' and resid 1050 through 1058 Processing helix chain 'E' and resid 1059 through 1106 removed outlier: 4.885A pdb=" N ALA E1065 " --> pdb=" O LEU E1061 " (cutoff:3.500A) Processing helix chain 'E' and resid 1198 through 1200 No H-bonds generated for 'chain 'E' and resid 1198 through 1200' Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 209 through 213 Processing helix chain 'J' and resid 222 through 231 removed outlier: 3.869A pdb=" N TYR J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 675 through 682 removed outlier: 6.699A pdb=" N CYS J 679 " --> pdb=" O SER J 676 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU J 680 " --> pdb=" O VAL J 677 " (cutoff:3.500A) Processing helix chain 'J' and resid 694 through 702 removed outlier: 5.047A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'I' and resid 805 through 811 removed outlier: 3.848A pdb=" N CYS I 811 " --> pdb=" O LYS I 807 " (cutoff:3.500A) Processing helix chain 'I' and resid 814 through 822 Processing helix chain 'I' and resid 824 through 854 removed outlier: 3.886A pdb=" N CYS I 828 " --> pdb=" O TYR I 824 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER I 852 " --> pdb=" O ASN I 848 " (cutoff:3.500A) Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 908 through 913 removed outlier: 3.531A pdb=" N MET I 913 " --> pdb=" O ASP I 910 " (cutoff:3.500A) Processing helix chain 'I' and resid 926 through 931 Processing helix chain 'I' and resid 939 through 953 removed outlier: 4.041A pdb=" N MET I 943 " --> pdb=" O MET I 939 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 982 Processing helix chain 'I' and resid 986 through 1007 removed outlier: 5.728A pdb=" N LYS I 995 " --> pdb=" O SER I 991 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU I 996 " --> pdb=" O GLU I 992 " (cutoff:3.500A) Processing helix chain 'I' and resid 1007 through 1012 removed outlier: 3.989A pdb=" N PHE I1012 " --> pdb=" O MET I1008 " (cutoff:3.500A) Processing helix chain 'I' and resid 1016 through 1039 Processing helix chain 'I' and resid 1040 through 1042 No H-bonds generated for 'chain 'I' and resid 1040 through 1042' Processing helix chain 'I' and resid 1050 through 1058 Processing helix chain 'I' and resid 1059 through 1106 removed outlier: 4.885A pdb=" N ALA I1065 " --> pdb=" O LEU I1061 " (cutoff:3.500A) Processing helix chain 'I' and resid 1198 through 1200 No H-bonds generated for 'chain 'I' and resid 1198 through 1200' Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 209 through 213 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.869A pdb=" N TYR F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 675 through 682 removed outlier: 6.699A pdb=" N CYS F 679 " --> pdb=" O SER F 676 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU F 680 " --> pdb=" O VAL F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 702 removed outlier: 5.047A pdb=" N ARG F 700 " --> pdb=" O MET F 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 719 through 724 removed outlier: 6.990A pdb=" N LEU A 759 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.680A pdb=" N ILE A 768 " --> pdb=" O SER E 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 5.623A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 785 through 796 removed outlier: 5.108A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 5.509A pdb=" N ASN A1163 " --> pdb=" O ASP A1157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.383A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.735A pdb=" N THR B 63 " --> pdb=" O TYR F 632 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL F 631 " --> pdb=" O VAL F 639 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL F 639 " --> pdb=" O LEU F 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 75 removed outlier: 3.964A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.884A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.174A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.165A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.661A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'B' and resid 214 through 215 removed outlier: 4.011A pdb=" N SER B 215 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 361 through 366 removed outlier: 5.522A pdb=" N SER B 362 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL B 661 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B 364 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 659 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.147A pdb=" N GLU B 605 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 617 through 619 removed outlier: 5.208A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY H 96 " --> pdb=" O MET H 100A" (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET H 100A" --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS L 49 " --> pdb=" O MET L 33 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 719 through 724 removed outlier: 6.990A pdb=" N LEU E 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU J 722 " --> pdb=" O LEU E 759 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU J 735 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 768 through 769 removed outlier: 5.680A pdb=" N ILE E 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 777 through 782 removed outlier: 5.623A pdb=" N VAL E1150 " --> pdb=" O LYS E1174 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE E1172 " --> pdb=" O ALA E1152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 785 through 796 removed outlier: 5.108A pdb=" N VAL E1124 " --> pdb=" O VAL E1139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 802 through 804 Processing sheet with id=AD4, first strand: chain 'E' and resid 1202 through 1204 removed outlier: 5.508A pdb=" N ASN E1163 " --> pdb=" O ASP E1157 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 33 through 35 removed outlier: 6.383A pdb=" N ASP J 34 " --> pdb=" O VAL J 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 67 through 75 removed outlier: 3.964A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 83 through 85 removed outlier: 5.884A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.174A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR J 206 " --> pdb=" O SER J 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 110 through 111 removed outlier: 6.165A pdb=" N LEU J 180 " --> pdb=" O TYR J 241 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR J 241 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA J 182 " --> pdb=" O PHE J 239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE J 239 " --> pdb=" O ALA J 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR J 184 " --> pdb=" O CYS J 237 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS J 237 " --> pdb=" O TYR J 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 127 through 129 removed outlier: 3.661A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'J' and resid 214 through 215 removed outlier: 4.011A pdb=" N SER J 215 " --> pdb=" O ASN J 218 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 361 through 366 removed outlier: 5.522A pdb=" N SER J 362 " --> pdb=" O VAL J 661 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL J 661 " --> pdb=" O SER J 362 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER J 364 " --> pdb=" O VAL J 659 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL J 659 " --> pdb=" O SER J 364 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 371 through 376 removed outlier: 4.147A pdb=" N GLU J 605 " --> pdb=" O GLY J 372 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 617 through 619 removed outlier: 5.208A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.417A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR C 33 " --> pdb=" O GLY C 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.417A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY C 96 " --> pdb=" O MET C 100A" (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET C 100A" --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET G 33 " --> pdb=" O HIS G 49 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N HIS G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 719 through 724 removed outlier: 6.990A pdb=" N LEU I 759 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 722 " --> pdb=" O LEU I 759 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU F 735 " --> pdb=" O LEU F 731 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 777 through 782 removed outlier: 5.623A pdb=" N VAL I1150 " --> pdb=" O LYS I1174 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 785 through 796 removed outlier: 5.108A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 802 through 804 Processing sheet with id=AF8, first strand: chain 'I' and resid 1202 through 1204 removed outlier: 5.509A pdb=" N ASN I1163 " --> pdb=" O ASP I1157 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 33 through 35 removed outlier: 6.383A pdb=" N ASP F 34 " --> pdb=" O VAL F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 67 through 75 removed outlier: 3.964A pdb=" N ARG F 335 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 83 through 85 removed outlier: 5.885A pdb=" N SER F 267 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN F 280 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 88 through 89 removed outlier: 7.174A pdb=" N SER F 88 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR F 206 " --> pdb=" O SER F 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 110 through 111 removed outlier: 6.165A pdb=" N LEU F 180 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR F 241 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA F 182 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE F 239 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR F 184 " --> pdb=" O CYS F 237 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS F 237 " --> pdb=" O TYR F 184 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.661A pdb=" N ALA F 309 " --> pdb=" O THR F 139 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AG7, first strand: chain 'F' and resid 214 through 215 removed outlier: 4.011A pdb=" N SER F 215 " --> pdb=" O ASN F 218 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 361 through 366 removed outlier: 5.522A pdb=" N SER F 362 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL F 661 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER F 364 " --> pdb=" O VAL F 659 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL F 659 " --> pdb=" O SER F 364 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 371 through 376 removed outlier: 4.147A pdb=" N GLU F 605 " --> pdb=" O GLY F 372 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AH2, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TYR D 33 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY D 96 " --> pdb=" O MET D 100A" (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET D 100A" --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.397A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET K 33 " --> pdb=" O HIS K 49 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS K 49 " --> pdb=" O MET K 33 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.397A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5741 1.32 - 1.46: 9910 1.46 - 1.59: 13437 1.59 - 1.73: 33 1.73 - 1.87: 192 Bond restraints: 29313 Sorted by residual: bond pdb=" CG GLN F 280 " pdb=" CD GLN F 280 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.92e+01 bond pdb=" CG GLN J 280 " pdb=" CD GLN J 280 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" CG GLN B 280 " pdb=" CD GLN B 280 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" CB TYR J 58 " pdb=" CG TYR J 58 " ideal model delta sigma weight residual 1.512 1.403 0.109 2.20e-02 2.07e+03 2.45e+01 bond pdb=" CB TYR B 58 " pdb=" CG TYR B 58 " ideal model delta sigma weight residual 1.512 1.403 0.109 2.20e-02 2.07e+03 2.45e+01 ... (remaining 29308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 34247 2.51 - 5.01: 4779 5.01 - 7.52: 697 7.52 - 10.02: 83 10.02 - 12.53: 19 Bond angle restraints: 39825 Sorted by residual: angle pdb=" N GLU F 367 " pdb=" CA GLU F 367 " pdb=" C GLU F 367 " ideal model delta sigma weight residual 111.07 121.18 -10.11 1.07e+00 8.73e-01 8.93e+01 angle pdb=" N GLU J 367 " pdb=" CA GLU J 367 " pdb=" C GLU J 367 " ideal model delta sigma weight residual 111.07 121.18 -10.11 1.07e+00 8.73e-01 8.93e+01 angle pdb=" N GLU B 367 " pdb=" CA GLU B 367 " pdb=" C GLU B 367 " ideal model delta sigma weight residual 111.07 121.17 -10.10 1.07e+00 8.73e-01 8.91e+01 angle pdb=" N VAL E 802 " pdb=" CA VAL E 802 " pdb=" C VAL E 802 " ideal model delta sigma weight residual 108.45 120.98 -12.53 1.48e+00 4.57e-01 7.17e+01 angle pdb=" N VAL A 802 " pdb=" CA VAL A 802 " pdb=" C VAL A 802 " ideal model delta sigma weight residual 108.45 120.97 -12.52 1.48e+00 4.57e-01 7.15e+01 ... (remaining 39820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 16085 16.91 - 33.82: 466 33.82 - 50.73: 110 50.73 - 67.64: 79 67.64 - 84.55: 42 Dihedral angle restraints: 16782 sinusoidal: 6414 harmonic: 10368 Sorted by residual: dihedral pdb=" CB CYS B 727 " pdb=" SG CYS B 727 " pdb=" SG CYS B 736 " pdb=" CB CYS B 736 " ideal model delta sinusoidal sigma weight residual 93.00 139.68 -46.68 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS F 727 " pdb=" SG CYS F 727 " pdb=" SG CYS F 736 " pdb=" CB CYS F 736 " ideal model delta sinusoidal sigma weight residual 93.00 139.66 -46.66 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS J 727 " pdb=" SG CYS J 727 " pdb=" SG CYS J 736 " pdb=" CB CYS J 736 " ideal model delta sinusoidal sigma weight residual 93.00 139.66 -46.66 1 1.00e+01 1.00e-02 3.01e+01 ... (remaining 16779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3078 0.093 - 0.185: 1200 0.185 - 0.278: 303 0.278 - 0.370: 56 0.370 - 0.463: 10 Chirality restraints: 4647 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 4644 not shown) Planarity restraints: 5103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 66 " -0.061 2.00e-02 2.50e+03 6.35e-02 5.04e+01 pdb=" CG ASN F 66 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN F 66 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN F 66 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG F 803 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 66 " 0.061 2.00e-02 2.50e+03 6.35e-02 5.03e+01 pdb=" CG ASN J 66 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN J 66 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN J 66 " -0.100 2.00e-02 2.50e+03 pdb=" C1 NAG J 803 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 66 " 0.061 2.00e-02 2.50e+03 6.34e-02 5.03e+01 pdb=" CG ASN B 66 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 66 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 66 " -0.100 2.00e-02 2.50e+03 pdb=" C1 NAG B 803 " 0.075 2.00e-02 2.50e+03 ... (remaining 5100 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6388 2.78 - 3.31: 26777 3.31 - 3.84: 50574 3.84 - 4.37: 61300 4.37 - 4.90: 97567 Nonbonded interactions: 242606 Sorted by model distance: nonbonded pdb=" OG SER J 328 " pdb=" OD1 ASP J 330 " model vdw 2.247 3.040 nonbonded pdb=" OG SER F 328 " pdb=" OD1 ASP F 330 " model vdw 2.247 3.040 nonbonded pdb=" OG SER B 328 " pdb=" OD1 ASP B 330 " model vdw 2.247 3.040 nonbonded pdb=" O4 NAG e 2 " pdb=" O6 NAG e 2 " model vdw 2.267 3.040 nonbonded pdb=" O4 NAG O 2 " pdb=" O6 NAG O 2 " model vdw 2.268 3.040 ... (remaining 242601 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'j' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'g' } ncs_group { reference = chain 'S' selection = chain 'a' selection = chain 'i' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.340 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 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 : 0.018 0.273 29433 Z= 0.955 Angle : 1.830 12.531 40143 Z= 1.200 Chirality : 0.103 0.463 4647 Planarity : 0.010 0.056 5061 Dihedral : 11.123 84.546 10044 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.22 % Favored : 96.19 % Rotamer: Outliers : 0.30 % Allowed : 1.02 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 3543 helix: -0.19 (0.17), residues: 666 sheet: 0.21 (0.17), residues: 867 loop : 0.55 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I1088 TYR 0.074 0.010 TYR E 909 PHE 0.044 0.007 PHE I1012 TRP 0.031 0.008 TRP F 44 HIS 0.010 0.002 HIS A1146 Details of bonding type rmsd/Z covalent geometry : bond 0.01759 / 0.94 (29313) covalent geometry : angle 1.81954 / 1.20 (39825) SS BOND : bond 0.07411 / 4.49 ( 42) SS BOND : angle 2.98151 / 2.05 ( 84) hydrogen bonds : bond 0.17085 / 11.56 ( 1154) hydrogen bonds : angle 7.41161 / 5.30 ( 3024) link_ALPHA1-3 : bond 0.07135 / 3.30 ( 3) link_ALPHA1-3 : angle 2.89356 / 1.65 ( 9) link_ALPHA1-6 : bond 0.05930 / 2.74 ( 3) link_ALPHA1-6 : angle 2.86095 / 1.63 ( 9) link_BETA1-4 : bond 0.05881 / 3.76 ( 30) link_BETA1-4 : angle 3.13746 / 2.22 ( 90) link_NAG-ASN : bond 0.04877 / 3.14 ( 42) link_NAG-ASN : angle 2.62562 / 1.90 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 627 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 GLN cc_start: 0.9180 (tp40) cc_final: 0.8764 (tp-100) REVERT: A 906 MET cc_start: 0.1475 (ttm) cc_final: 0.0215 (tmm) REVERT: A 1027 ASN cc_start: 0.8147 (m-40) cc_final: 0.7866 (m-40) REVERT: A 1074 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6648 (tpm170) REVERT: A 1126 PHE cc_start: 0.7280 (m-80) cc_final: 0.6766 (m-80) REVERT: B 18 TYR cc_start: 0.7902 (m-80) cc_final: 0.6361 (p90) REVERT: B 156 PHE cc_start: 0.7915 (m-80) cc_final: 0.7487 (m-80) REVERT: B 183 PHE cc_start: 0.9077 (p90) cc_final: 0.8776 (p90) REVERT: B 243 TYR cc_start: 0.8504 (m-80) cc_final: 0.7869 (m-80) REVERT: B 293 TYR cc_start: 0.6939 (p90) cc_final: 0.6548 (p90) REVERT: B 354 PHE cc_start: 0.5861 (p90) cc_final: 0.5636 (p90) REVERT: B 674 PHE cc_start: 0.8651 (m-80) cc_final: 0.8334 (m-80) REVERT: H 63 PHE cc_start: 0.4976 (m-80) cc_final: 0.4771 (m-80) REVERT: L 103 LYS cc_start: 0.6745 (tttt) cc_final: 0.6453 (mmtm) REVERT: E 808 GLN cc_start: 0.9218 (tp40) cc_final: 0.8828 (tp-100) REVERT: E 906 MET cc_start: 0.1885 (ttm) cc_final: 0.0994 (tmm) REVERT: E 1027 ASN cc_start: 0.8006 (m-40) cc_final: 0.7640 (m-40) REVERT: E 1074 ARG cc_start: 0.7523 (mmt90) cc_final: 0.6927 (tpp-160) REVERT: E 1126 PHE cc_start: 0.7307 (m-80) cc_final: 0.6879 (m-80) REVERT: J 18 TYR cc_start: 0.7989 (m-80) cc_final: 0.6205 (p90) REVERT: J 116 PHE cc_start: 0.7338 (p90) cc_final: 0.7131 (p90) REVERT: J 156 PHE cc_start: 0.7890 (m-80) cc_final: 0.7472 (m-80) REVERT: J 183 PHE cc_start: 0.9001 (p90) cc_final: 0.8706 (p90) REVERT: J 228 PHE cc_start: 0.9497 (t80) cc_final: 0.9212 (t80) REVERT: J 243 TYR cc_start: 0.8518 (m-80) cc_final: 0.7692 (m-80) REVERT: J 278 MET cc_start: 0.4808 (ttm) cc_final: 0.4542 (mtp) REVERT: J 293 TYR cc_start: 0.6695 (p90) cc_final: 0.6386 (p90) REVERT: J 632 TYR cc_start: 0.8285 (m-80) cc_final: 0.8082 (m-80) REVERT: J 674 PHE cc_start: 0.8579 (m-80) cc_final: 0.8284 (m-80) REVERT: C 82 PHE cc_start: 0.7965 (m-80) cc_final: 0.7628 (m-10) REVERT: G 103 LYS cc_start: 0.6567 (tttt) cc_final: 0.6342 (mmtm) REVERT: I 757 MET cc_start: 0.5570 (mtt) cc_final: 0.5260 (mmt) REVERT: I 808 GLN cc_start: 0.9171 (tp40) cc_final: 0.8752 (tp-100) REVERT: I 893 LEU cc_start: 0.8692 (mt) cc_final: 0.8283 (mt) REVERT: I 906 MET cc_start: 0.2209 (ttm) cc_final: 0.1152 (tmm) REVERT: I 1027 ASN cc_start: 0.8016 (m-40) cc_final: 0.7648 (m-40) REVERT: I 1123 ILE cc_start: 0.8830 (tp) cc_final: 0.8523 (tp) REVERT: I 1126 PHE cc_start: 0.7282 (m-80) cc_final: 0.6884 (m-80) REVERT: F 183 PHE cc_start: 0.9037 (p90) cc_final: 0.8700 (p90) REVERT: F 228 PHE cc_start: 0.9538 (t80) cc_final: 0.9300 (t80) REVERT: F 243 TYR cc_start: 0.8243 (m-80) cc_final: 0.7625 (m-80) REVERT: F 293 TYR cc_start: 0.6695 (p90) cc_final: 0.6345 (p90) REVERT: F 354 PHE cc_start: 0.5817 (p90) cc_final: 0.5565 (p90) REVERT: F 674 PHE cc_start: 0.8599 (m-80) cc_final: 0.8278 (m-80) REVERT: D 37 LEU cc_start: 0.6386 (mp) cc_final: 0.6163 (mp) REVERT: D 50 TRP cc_start: 0.7222 (p90) cc_final: 0.6338 (p90) REVERT: D 82 PHE cc_start: 0.7830 (m-80) cc_final: 0.7434 (m-10) REVERT: K 103 LYS cc_start: 0.6472 (tttt) cc_final: 0.6236 (mmtm) outliers start: 9 outliers final: 5 residues processed: 636 average time/residue: 0.1987 time to fit residues: 197.5425 Evaluate side-chains 336 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 331 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 839 ASN A1084 GLN A1132 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B 637 ASN H 68 GLN E1084 GLN E1129 ASN ** E1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN J 637 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1084 GLN I1129 ASN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN F 637 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.083657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.064028 restraints weight = 201309.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.065013 restraints weight = 168482.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.065837 restraints weight = 140201.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.066583 restraints weight = 120075.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.067024 restraints weight = 108472.219| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29433 Z= 0.199 Angle : 0.802 11.538 40143 Z= 0.422 Chirality : 0.049 0.317 4647 Planarity : 0.006 0.057 5061 Dihedral : 5.814 24.189 3873 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.78 % Favored : 95.96 % Rotamer: Outliers : 0.30 % Allowed : 2.70 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3543 helix: 0.59 (0.19), residues: 687 sheet: 0.08 (0.17), residues: 867 loop : 0.01 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 822 TYR 0.045 0.002 TYR E 909 PHE 0.024 0.003 PHE E 895 TRP 0.045 0.003 TRP H 50 HIS 0.008 0.001 HIS F 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (29313) covalent geometry : angle 0.77320 / 0.42 (39825) SS BOND : bond 0.01116 / 0.69 ( 42) SS BOND : angle 1.12321 / 0.70 ( 84) hydrogen bonds : bond 0.06316 / 4.25 ( 1154) hydrogen bonds : angle 6.21603 / 4.44 ( 3024) link_ALPHA1-3 : bond 0.00286 / 0.15 ( 3) link_ALPHA1-3 : angle 1.20514 / 0.65 ( 9) link_ALPHA1-6 : bond 0.00068 / 0.03 ( 3) link_ALPHA1-6 : angle 1.80082 / 0.95 ( 9) link_BETA1-4 : bond 0.00450 / 0.31 ( 30) link_BETA1-4 : angle 2.04007 / 1.40 ( 90) link_NAG-ASN : bond 0.00561 / 0.36 ( 42) link_NAG-ASN : angle 3.44229 / 2.51 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 419 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.5940 (mmt) cc_final: 0.4624 (mmt) REVERT: A 808 GLN cc_start: 0.9142 (tp40) cc_final: 0.8721 (tp-100) REVERT: A 906 MET cc_start: 0.1084 (ttm) cc_final: 0.0557 (tmm) REVERT: A 1027 ASN cc_start: 0.8175 (m-40) cc_final: 0.7803 (m-40) REVERT: A 1074 ARG cc_start: 0.7316 (mmt90) cc_final: 0.6664 (tpm170) REVERT: A 1090 GLU cc_start: 0.7776 (mm-30) cc_final: 0.6987 (pp20) REVERT: A 1101 ASP cc_start: 0.8731 (m-30) cc_final: 0.8471 (t0) REVERT: A 1102 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8291 (mmtt) REVERT: B 156 PHE cc_start: 0.8070 (m-80) cc_final: 0.7518 (m-80) REVERT: B 172 LEU cc_start: 0.7941 (tp) cc_final: 0.7644 (tp) REVERT: B 183 PHE cc_start: 0.8373 (p90) cc_final: 0.8129 (p90) REVERT: B 243 TYR cc_start: 0.7966 (m-80) cc_final: 0.7262 (m-80) REVERT: B 293 TYR cc_start: 0.7349 (p90) cc_final: 0.6873 (p90) REVERT: B 354 PHE cc_start: 0.5547 (p90) cc_final: 0.5258 (p90) REVERT: B 652 ARG cc_start: 0.6312 (tpt170) cc_final: 0.6020 (tpt170) REVERT: B 674 PHE cc_start: 0.8444 (m-80) cc_final: 0.8069 (m-80) REVERT: H 80 MET cc_start: 0.3950 (ttm) cc_final: 0.2617 (ttm) REVERT: E 757 MET cc_start: 0.5922 (mmt) cc_final: 0.4810 (mmt) REVERT: E 808 GLN cc_start: 0.9224 (tp40) cc_final: 0.8749 (tp-100) REVERT: E 906 MET cc_start: 0.0950 (ttm) cc_final: 0.0555 (tmm) REVERT: E 1027 ASN cc_start: 0.8104 (m-40) cc_final: 0.7746 (m-40) REVERT: E 1090 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7032 (pp20) REVERT: E 1101 ASP cc_start: 0.8590 (m-30) cc_final: 0.8385 (t0) REVERT: E 1102 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8304 (mmtt) REVERT: J 69 ILE cc_start: 0.6081 (tp) cc_final: 0.5673 (tp) REVERT: J 156 PHE cc_start: 0.8031 (m-80) cc_final: 0.7551 (m-80) REVERT: J 172 LEU cc_start: 0.7795 (tp) cc_final: 0.7435 (tp) REVERT: J 183 PHE cc_start: 0.8473 (p90) cc_final: 0.8087 (p90) REVERT: J 243 TYR cc_start: 0.7960 (m-80) cc_final: 0.7206 (m-80) REVERT: J 293 TYR cc_start: 0.7283 (p90) cc_final: 0.6573 (p90) REVERT: J 632 TYR cc_start: 0.8368 (m-80) cc_final: 0.8113 (m-80) REVERT: J 652 ARG cc_start: 0.6211 (tpt170) cc_final: 0.5967 (tpt170) REVERT: J 674 PHE cc_start: 0.8356 (m-80) cc_final: 0.7968 (m-80) REVERT: C 36 TRP cc_start: 0.5688 (m100) cc_final: 0.5469 (m-10) REVERT: C 58 GLU cc_start: 0.8379 (tp30) cc_final: 0.7970 (tp30) REVERT: C 80 MET cc_start: 0.3861 (ttm) cc_final: 0.3045 (ttm) REVERT: C 82 PHE cc_start: 0.8732 (m-80) cc_final: 0.8068 (m-10) REVERT: G 47 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5668 (mt) REVERT: I 757 MET cc_start: 0.6326 (mtt) cc_final: 0.5663 (mmt) REVERT: I 863 PRO cc_start: 0.7539 (Cg_exo) cc_final: 0.7322 (Cg_endo) REVERT: I 893 LEU cc_start: 0.8431 (mt) cc_final: 0.8051 (mt) REVERT: I 900 ILE cc_start: 0.4859 (pt) cc_final: 0.4633 (pt) REVERT: I 906 MET cc_start: 0.1189 (ttm) cc_final: 0.0814 (tmm) REVERT: I 943 MET cc_start: 0.8068 (tpp) cc_final: 0.7863 (tpt) REVERT: I 1027 ASN cc_start: 0.7778 (m-40) cc_final: 0.7427 (m-40) REVERT: I 1090 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6879 (pp20) REVERT: I 1101 ASP cc_start: 0.8622 (m-30) cc_final: 0.8390 (t0) REVERT: I 1102 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8328 (mmtt) REVERT: F 69 ILE cc_start: 0.6409 (tp) cc_final: 0.5933 (tp) REVERT: F 116 PHE cc_start: 0.6592 (p90) cc_final: 0.6365 (p90) REVERT: F 156 PHE cc_start: 0.7450 (m-10) cc_final: 0.7070 (m-10) REVERT: F 172 LEU cc_start: 0.8117 (tp) cc_final: 0.7849 (tp) REVERT: F 183 PHE cc_start: 0.8398 (p90) cc_final: 0.8046 (p90) REVERT: F 243 TYR cc_start: 0.7771 (m-80) cc_final: 0.7156 (m-80) REVERT: F 278 MET cc_start: 0.4863 (mmm) cc_final: 0.2560 (mmm) REVERT: F 293 TYR cc_start: 0.7139 (p90) cc_final: 0.6444 (p90) REVERT: F 351 TYR cc_start: 0.7429 (m-10) cc_final: 0.7017 (m-10) REVERT: F 354 PHE cc_start: 0.5035 (p90) cc_final: 0.4757 (p90) REVERT: F 652 ARG cc_start: 0.6449 (tpt170) cc_final: 0.6221 (tpt170) REVERT: F 674 PHE cc_start: 0.8491 (m-80) cc_final: 0.8094 (m-80) REVERT: D 18 VAL cc_start: 0.9518 (p) cc_final: 0.9241 (p) REVERT: D 36 TRP cc_start: 0.5422 (m100) cc_final: 0.4732 (m-10) REVERT: D 58 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7197 (mm-30) REVERT: D 80 MET cc_start: 0.4586 (ttm) cc_final: 0.3768 (ttm) REVERT: D 82 PHE cc_start: 0.8576 (m-80) cc_final: 0.7989 (m-10) outliers start: 9 outliers final: 2 residues processed: 428 average time/residue: 0.1854 time to fit residues: 126.9821 Evaluate side-chains 297 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 294 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 246 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 339 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 161 optimal weight: 50.0000 overall best weight: 5.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN A1129 ASN A1132 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN H 68 GLN H 81 GLN ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1084 GLN ** E1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1163 ASN ** E1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 ASN J 346 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1066 GLN I1084 GLN ** I1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1163 ASN I1169 ASN ** I1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 346 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.079491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.060710 restraints weight = 211924.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.061629 restraints weight = 181412.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.062185 restraints weight = 151306.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.062777 restraints weight = 132334.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.062777 restraints weight = 119033.090| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 29433 Z= 0.249 Angle : 0.837 12.590 40143 Z= 0.432 Chirality : 0.048 0.421 4647 Planarity : 0.006 0.059 5061 Dihedral : 6.034 25.714 3873 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.49 % Favored : 95.17 % Rotamer: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 3543 helix: -0.43 (0.18), residues: 678 sheet: -0.31 (0.17), residues: 744 loop : -0.50 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 979 TYR 0.038 0.003 TYR I 909 PHE 0.023 0.003 PHE I1012 TRP 0.057 0.004 TRP H 50 HIS 0.010 0.002 HIS E1146 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.25 (29313) covalent geometry : angle 0.81885 / 0.43 (39825) SS BOND : bond 0.00595 / 0.36 ( 42) SS BOND : angle 1.20808 / 0.77 ( 84) hydrogen bonds : bond 0.05919 / 3.91 ( 1154) hydrogen bonds : angle 6.57842 / 4.70 ( 3024) link_ALPHA1-3 : bond 0.00994 / 0.46 ( 3) link_ALPHA1-3 : angle 0.92319 / 0.55 ( 9) link_ALPHA1-6 : bond 0.00069 / 0.03 ( 3) link_ALPHA1-6 : angle 1.66014 / 0.87 ( 9) link_BETA1-4 : bond 0.00472 / 0.32 ( 30) link_BETA1-4 : angle 1.89895 / 1.25 ( 90) link_NAG-ASN : bond 0.00609 / 0.38 ( 42) link_NAG-ASN : angle 2.69634 / 1.93 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 346 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.6117 (mmt) cc_final: 0.5162 (mmt) REVERT: A 906 MET cc_start: 0.1127 (ttm) cc_final: 0.0491 (tmm) REVERT: A 943 MET cc_start: 0.7660 (tpt) cc_final: 0.7233 (tpt) REVERT: A 1026 VAL cc_start: 0.8441 (t) cc_final: 0.8227 (t) REVERT: A 1027 ASN cc_start: 0.8219 (m-40) cc_final: 0.7793 (m-40) REVERT: A 1074 ARG cc_start: 0.7540 (mmt90) cc_final: 0.7007 (tpp-160) REVERT: A 1090 GLU cc_start: 0.8057 (mm-30) cc_final: 0.6905 (pp20) REVERT: B 172 LEU cc_start: 0.7890 (tp) cc_final: 0.7615 (tp) REVERT: B 183 PHE cc_start: 0.8562 (p90) cc_final: 0.8305 (p90) REVERT: B 243 TYR cc_start: 0.7808 (m-80) cc_final: 0.7234 (m-80) REVERT: B 266 PHE cc_start: 0.8900 (m-80) cc_final: 0.8692 (m-80) REVERT: B 278 MET cc_start: 0.4888 (tpt) cc_final: 0.1161 (ttt) REVERT: B 293 TYR cc_start: 0.7324 (p90) cc_final: 0.6506 (p90) REVERT: H 80 MET cc_start: 0.5918 (ttm) cc_final: 0.4666 (ttm) REVERT: H 82 PHE cc_start: 0.9145 (m-80) cc_final: 0.8750 (m-10) REVERT: E 757 MET cc_start: 0.5956 (mmt) cc_final: 0.5091 (mmt) REVERT: E 788 PHE cc_start: 0.7375 (m-80) cc_final: 0.7174 (m-80) REVERT: E 893 LEU cc_start: 0.8857 (mt) cc_final: 0.8264 (mt) REVERT: E 906 MET cc_start: 0.0634 (ttm) cc_final: 0.0327 (tmm) REVERT: E 1027 ASN cc_start: 0.8182 (m-40) cc_final: 0.7821 (m110) REVERT: E 1090 GLU cc_start: 0.8062 (mm-30) cc_final: 0.6874 (pp20) REVERT: E 1123 ILE cc_start: 0.9048 (tp) cc_final: 0.8511 (tt) REVERT: J 116 PHE cc_start: 0.6712 (p90) cc_final: 0.6309 (p90) REVERT: J 172 LEU cc_start: 0.7966 (tp) cc_final: 0.7640 (tp) REVERT: J 183 PHE cc_start: 0.8578 (p90) cc_final: 0.8331 (p90) REVERT: J 243 TYR cc_start: 0.7863 (m-80) cc_final: 0.7214 (m-80) REVERT: J 293 TYR cc_start: 0.7494 (p90) cc_final: 0.6792 (p90) REVERT: C 82 PHE cc_start: 0.9045 (m-80) cc_final: 0.8527 (m-10) REVERT: G 32 PHE cc_start: 0.6641 (m-80) cc_final: 0.6359 (t80) REVERT: I 757 MET cc_start: 0.6342 (mtt) cc_final: 0.6036 (mtt) REVERT: I 809 TYR cc_start: 0.7234 (t80) cc_final: 0.6998 (t80) REVERT: I 848 ASN cc_start: 0.8740 (m-40) cc_final: 0.8538 (m-40) REVERT: I 893 LEU cc_start: 0.8521 (mt) cc_final: 0.7988 (mt) REVERT: I 906 MET cc_start: 0.0829 (ttm) cc_final: 0.0564 (tmm) REVERT: I 1027 ASN cc_start: 0.8082 (m-40) cc_final: 0.7732 (m-40) REVERT: I 1074 ARG cc_start: 0.7747 (mmt90) cc_final: 0.7103 (tpm170) REVERT: I 1090 GLU cc_start: 0.8157 (mm-30) cc_final: 0.6861 (pp20) REVERT: I 1123 ILE cc_start: 0.9142 (tp) cc_final: 0.8615 (tt) REVERT: F 108 ASP cc_start: 0.6709 (m-30) cc_final: 0.6335 (m-30) REVERT: F 172 LEU cc_start: 0.7951 (tp) cc_final: 0.7693 (tp) REVERT: F 183 PHE cc_start: 0.8524 (p90) cc_final: 0.8290 (p90) REVERT: F 187 LEU cc_start: 0.8080 (pt) cc_final: 0.7641 (pt) REVERT: F 243 TYR cc_start: 0.7786 (m-80) cc_final: 0.7227 (m-80) REVERT: F 266 PHE cc_start: 0.8742 (m-80) cc_final: 0.8336 (m-80) REVERT: F 278 MET cc_start: 0.5647 (mmm) cc_final: 0.2645 (mmm) REVERT: F 293 TYR cc_start: 0.7496 (p90) cc_final: 0.6655 (p90) REVERT: F 696 MET cc_start: 0.2534 (ptt) cc_final: 0.2072 (ptt) REVERT: D 18 VAL cc_start: 0.9582 (p) cc_final: 0.9287 (p) REVERT: D 36 TRP cc_start: 0.5648 (m100) cc_final: 0.5206 (m-10) REVERT: D 80 MET cc_start: 0.5145 (ttm) cc_final: 0.4143 (ttm) REVERT: D 82 PHE cc_start: 0.9018 (m-80) cc_final: 0.8398 (m-10) outliers start: 2 outliers final: 0 residues processed: 347 average time/residue: 0.1850 time to fit residues: 102.9517 Evaluate side-chains 258 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 177 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 256 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 240 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 53 optimal weight: 40.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 792 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 792 GLN ** E 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1084 GLN ** E1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN ** J 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 792 GLN ** I 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 GLN I1084 GLN ** I1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN ** F 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.077465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.059438 restraints weight = 218604.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.060142 restraints weight = 188070.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.060660 restraints weight = 164204.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.060660 restraints weight = 141920.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.060660 restraints weight = 141920.122| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 29433 Z= 0.265 Angle : 0.844 14.339 40143 Z= 0.434 Chirality : 0.049 0.405 4647 Planarity : 0.006 0.051 5061 Dihedral : 6.315 26.230 3873 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 24.67 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.42 % Favored : 94.24 % Rotamer: Outliers : 0.20 % Allowed : 3.73 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -1.33 (0.13), residues: 3543 helix: -0.97 (0.17), residues: 699 sheet: -0.59 (0.17), residues: 729 loop : -0.92 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 979 TYR 0.037 0.003 TYR F 64 PHE 0.030 0.003 PHE E 788 TRP 0.061 0.003 TRP D 50 HIS 0.010 0.002 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.26 (29313) covalent geometry : angle 0.82816 / 0.43 (39825) SS BOND : bond 0.00631 / 0.37 ( 42) SS BOND : angle 1.12107 / 0.66 ( 84) hydrogen bonds : bond 0.05875 / 3.87 ( 1154) hydrogen bonds : angle 6.80709 / 4.86 ( 3024) link_ALPHA1-3 : bond 0.01299 / 0.60 ( 3) link_ALPHA1-3 : angle 1.09324 / 0.64 ( 9) link_ALPHA1-6 : bond 0.00042 / 0.02 ( 3) link_ALPHA1-6 : angle 1.62915 / 0.89 ( 9) link_BETA1-4 : bond 0.00324 / 0.19 ( 30) link_BETA1-4 : angle 1.97797 / 1.32 ( 90) link_NAG-ASN : bond 0.00689 / 0.44 ( 42) link_NAG-ASN : angle 2.49960 / 1.78 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 322 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.6371 (mmt) cc_final: 0.5425 (mmt) REVERT: A 893 LEU cc_start: 0.8775 (mt) cc_final: 0.8207 (mt) REVERT: A 906 MET cc_start: 0.1648 (ttm) cc_final: 0.0956 (tmm) REVERT: A 943 MET cc_start: 0.7781 (tpt) cc_final: 0.7398 (tpt) REVERT: A 955 ILE cc_start: 0.5682 (mm) cc_final: 0.5181 (mm) REVERT: B 108 ASP cc_start: 0.6345 (m-30) cc_final: 0.6135 (m-30) REVERT: B 156 PHE cc_start: 0.8067 (m-10) cc_final: 0.7854 (m-10) REVERT: B 172 LEU cc_start: 0.8066 (tp) cc_final: 0.7777 (tp) REVERT: B 180 LEU cc_start: 0.8895 (tt) cc_final: 0.8577 (mt) REVERT: B 183 PHE cc_start: 0.8570 (p90) cc_final: 0.8285 (p90) REVERT: B 243 TYR cc_start: 0.7815 (m-80) cc_final: 0.7408 (m-80) REVERT: B 278 MET cc_start: 0.6326 (tpp) cc_final: 0.4611 (ttm) REVERT: B 293 TYR cc_start: 0.7538 (p90) cc_final: 0.6779 (p90) REVERT: B 674 PHE cc_start: 0.8556 (m-80) cc_final: 0.8257 (m-10) REVERT: B 689 TYR cc_start: 0.8207 (p90) cc_final: 0.7980 (p90) REVERT: B 696 MET cc_start: 0.3174 (ptt) cc_final: 0.2890 (ptt) REVERT: H 82 PHE cc_start: 0.9148 (m-80) cc_final: 0.8894 (m-10) REVERT: E 757 MET cc_start: 0.6045 (mmt) cc_final: 0.5203 (mmt) REVERT: E 893 LEU cc_start: 0.8480 (mt) cc_final: 0.8072 (mt) REVERT: E 906 MET cc_start: 0.0877 (ttm) cc_final: 0.0571 (tmm) REVERT: E 1027 ASN cc_start: 0.8317 (m-40) cc_final: 0.6881 (p0) REVERT: E 1028 ASN cc_start: 0.8969 (t0) cc_final: 0.8739 (t0) REVERT: E 1074 ARG cc_start: 0.7528 (mmt90) cc_final: 0.7244 (tpm170) REVERT: J 108 ASP cc_start: 0.6500 (m-30) cc_final: 0.6287 (m-30) REVERT: J 116 PHE cc_start: 0.6938 (p90) cc_final: 0.6638 (p90) REVERT: J 172 LEU cc_start: 0.8015 (tp) cc_final: 0.7709 (tp) REVERT: J 180 LEU cc_start: 0.9032 (tt) cc_final: 0.8378 (mt) REVERT: J 183 PHE cc_start: 0.8683 (p90) cc_final: 0.8351 (p90) REVERT: J 293 TYR cc_start: 0.7512 (p90) cc_final: 0.6903 (p90) REVERT: J 674 PHE cc_start: 0.8538 (m-80) cc_final: 0.8328 (m-10) REVERT: J 696 MET cc_start: 0.2481 (ptt) cc_final: 0.1982 (ptt) REVERT: C 80 MET cc_start: 0.6209 (ttm) cc_final: 0.4763 (ttm) REVERT: C 82 PHE cc_start: 0.9359 (m-80) cc_final: 0.9103 (m-10) REVERT: I 757 MET cc_start: 0.6462 (mtt) cc_final: 0.5784 (mmt) REVERT: I 893 LEU cc_start: 0.8389 (mt) cc_final: 0.8059 (mt) REVERT: I 906 MET cc_start: 0.0798 (ttm) cc_final: 0.0594 (tmm) REVERT: I 943 MET cc_start: 0.8171 (tpp) cc_final: 0.7584 (tpt) REVERT: F 108 ASP cc_start: 0.6563 (m-30) cc_final: 0.6268 (m-30) REVERT: F 172 LEU cc_start: 0.8226 (tp) cc_final: 0.7941 (tp) REVERT: F 180 LEU cc_start: 0.9058 (tt) cc_final: 0.8709 (mt) REVERT: F 243 TYR cc_start: 0.7823 (m-80) cc_final: 0.7395 (m-80) REVERT: F 254 PHE cc_start: 0.6259 (t80) cc_final: 0.5964 (t80) REVERT: F 266 PHE cc_start: 0.8842 (m-80) cc_final: 0.8266 (m-80) REVERT: F 278 MET cc_start: 0.5661 (mmm) cc_final: 0.3033 (mmm) REVERT: F 293 TYR cc_start: 0.7616 (p90) cc_final: 0.6955 (p90) REVERT: F 327 PHE cc_start: 0.8004 (m-80) cc_final: 0.7684 (m-80) REVERT: F 674 PHE cc_start: 0.8521 (m-80) cc_final: 0.8245 (m-10) REVERT: F 686 MET cc_start: 0.5242 (mmp) cc_final: 0.4906 (mmm) REVERT: F 696 MET cc_start: 0.2541 (ptt) cc_final: 0.2152 (ptt) REVERT: D 18 VAL cc_start: 0.9614 (p) cc_final: 0.9337 (p) REVERT: D 36 TRP cc_start: 0.5857 (m100) cc_final: 0.5519 (m-10) REVERT: D 80 MET cc_start: 0.5776 (ttm) cc_final: 0.4611 (ttm) REVERT: D 82 PHE cc_start: 0.9175 (m-80) cc_final: 0.8626 (m-10) outliers start: 6 outliers final: 2 residues processed: 328 average time/residue: 0.1870 time to fit residues: 99.3300 Evaluate side-chains 249 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 89 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 320 optimal weight: 8.9990 chunk 348 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1066 GLN A1084 GLN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN H 68 GLN H 81 GLN E1084 GLN E1132 ASN ** E1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN J 628 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1084 GLN I1129 ASN I1132 ASN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN F 628 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.079496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.061481 restraints weight = 211062.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.062068 restraints weight = 181102.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.063110 restraints weight = 150004.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.063501 restraints weight = 128479.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.063501 restraints weight = 112655.523| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29433 Z= 0.151 Angle : 0.704 10.232 40143 Z= 0.357 Chirality : 0.046 0.461 4647 Planarity : 0.005 0.045 5061 Dihedral : 5.769 27.387 3873 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.97 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -1.16 (0.13), residues: 3543 helix: -0.41 (0.18), residues: 681 sheet: -0.58 (0.18), residues: 753 loop : -0.93 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 822 TYR 0.024 0.002 TYR I 909 PHE 0.019 0.002 PHE F 281 TRP 0.053 0.003 TRP H 50 HIS 0.004 0.001 HIS E1146 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (29313) covalent geometry : angle 0.67842 / 0.35 (39825) SS BOND : bond 0.00438 / 0.27 ( 42) SS BOND : angle 1.01317 / 0.68 ( 84) hydrogen bonds : bond 0.04885 / 3.28 ( 1154) hydrogen bonds : angle 6.29273 / 4.50 ( 3024) link_ALPHA1-3 : bond 0.01383 / 0.65 ( 3) link_ALPHA1-3 : angle 1.19290 / 0.69 ( 9) link_ALPHA1-6 : bond 0.00520 / 0.24 ( 3) link_ALPHA1-6 : angle 1.20741 / 0.69 ( 9) link_BETA1-4 : bond 0.00332 / 0.21 ( 30) link_BETA1-4 : angle 1.76996 / 1.17 ( 90) link_NAG-ASN : bond 0.00528 / 0.31 ( 42) link_NAG-ASN : angle 3.05831 / 2.17 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.6315 (mmt) cc_final: 0.5435 (mmt) REVERT: A 906 MET cc_start: 0.1697 (ttm) cc_final: 0.0945 (tmm) REVERT: A 913 MET cc_start: 0.8199 (mpp) cc_final: 0.7603 (mpp) REVERT: A 921 ARG cc_start: 0.5068 (ttm170) cc_final: 0.3129 (pmt-80) REVERT: A 943 MET cc_start: 0.7685 (tpt) cc_final: 0.7279 (tpt) REVERT: A 1021 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8571 (mmtm) REVERT: A 1090 GLU cc_start: 0.8193 (mm-30) cc_final: 0.6687 (pp20) REVERT: A 1102 LYS cc_start: 0.9096 (mmpt) cc_final: 0.8693 (mmmt) REVERT: B 108 ASP cc_start: 0.6052 (m-30) cc_final: 0.5775 (m-30) REVERT: B 116 PHE cc_start: 0.6857 (p90) cc_final: 0.6643 (p90) REVERT: B 172 LEU cc_start: 0.7859 (tp) cc_final: 0.7542 (tp) REVERT: B 180 LEU cc_start: 0.8872 (tt) cc_final: 0.8582 (mt) REVERT: B 183 PHE cc_start: 0.8452 (p90) cc_final: 0.8056 (p90) REVERT: B 228 PHE cc_start: 0.9226 (t80) cc_final: 0.8985 (t80) REVERT: B 243 TYR cc_start: 0.7881 (m-80) cc_final: 0.7463 (m-80) REVERT: B 254 PHE cc_start: 0.6527 (t80) cc_final: 0.6095 (t80) REVERT: B 256 ILE cc_start: 0.8400 (tt) cc_final: 0.8005 (mp) REVERT: B 266 PHE cc_start: 0.8869 (m-80) cc_final: 0.8587 (m-80) REVERT: B 278 MET cc_start: 0.6028 (tpp) cc_final: 0.4455 (ttm) REVERT: B 293 TYR cc_start: 0.7169 (p90) cc_final: 0.6875 (p90) REVERT: B 327 PHE cc_start: 0.8185 (m-80) cc_final: 0.7887 (m-80) REVERT: B 674 PHE cc_start: 0.8569 (m-80) cc_final: 0.8284 (m-10) REVERT: B 696 MET cc_start: 0.2919 (ptt) cc_final: 0.2577 (ptt) REVERT: H 80 MET cc_start: 0.6262 (ttm) cc_final: 0.4363 (ttm) REVERT: E 757 MET cc_start: 0.5919 (mmt) cc_final: 0.5134 (mmt) REVERT: E 906 MET cc_start: 0.0906 (ttm) cc_final: 0.0536 (tmm) REVERT: E 913 MET cc_start: 0.8001 (mpp) cc_final: 0.7396 (mpp) REVERT: E 921 ARG cc_start: 0.5043 (ttm170) cc_final: 0.3074 (pmt-80) REVERT: E 955 ILE cc_start: 0.5451 (mm) cc_final: 0.5212 (mm) REVERT: E 1027 ASN cc_start: 0.8164 (m-40) cc_final: 0.6674 (p0) REVERT: E 1090 GLU cc_start: 0.8046 (mm-30) cc_final: 0.6652 (pp20) REVERT: E 1101 ASP cc_start: 0.8560 (m-30) cc_final: 0.8349 (t70) REVERT: E 1102 LYS cc_start: 0.9098 (mmpt) cc_final: 0.8756 (mmmt) REVERT: J 108 ASP cc_start: 0.6214 (m-30) cc_final: 0.5950 (m-30) REVERT: J 116 PHE cc_start: 0.6714 (p90) cc_final: 0.6423 (p90) REVERT: J 172 LEU cc_start: 0.7856 (tp) cc_final: 0.7542 (tp) REVERT: J 183 PHE cc_start: 0.8567 (p90) cc_final: 0.8207 (p90) REVERT: J 278 MET cc_start: 0.5051 (tpp) cc_final: 0.3790 (ttm) REVERT: J 293 TYR cc_start: 0.7413 (p90) cc_final: 0.7210 (p90) REVERT: J 327 PHE cc_start: 0.8244 (m-80) cc_final: 0.7985 (m-80) REVERT: J 606 TYR cc_start: 0.7673 (p90) cc_final: 0.7351 (p90) REVERT: J 632 TYR cc_start: 0.8775 (m-80) cc_final: 0.8433 (m-80) REVERT: J 674 PHE cc_start: 0.8435 (m-80) cc_final: 0.8209 (m-10) REVERT: J 696 MET cc_start: 0.2332 (ptt) cc_final: 0.1873 (ptt) REVERT: C 80 MET cc_start: 0.6430 (ttm) cc_final: 0.4898 (ttm) REVERT: C 82 PHE cc_start: 0.9361 (m-80) cc_final: 0.9140 (m-10) REVERT: I 757 MET cc_start: 0.6353 (mtt) cc_final: 0.5620 (mmt) REVERT: I 809 TYR cc_start: 0.7350 (t80) cc_final: 0.6953 (t80) REVERT: I 921 ARG cc_start: 0.5328 (ttm170) cc_final: 0.3265 (pmt-80) REVERT: I 1021 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8584 (mmtm) REVERT: I 1074 ARG cc_start: 0.7569 (mmt90) cc_final: 0.7249 (tpp-160) REVERT: I 1090 GLU cc_start: 0.8116 (mm-30) cc_final: 0.6530 (pp20) REVERT: I 1102 LYS cc_start: 0.9085 (mmpt) cc_final: 0.8752 (mmmt) REVERT: F 108 ASP cc_start: 0.6302 (m-30) cc_final: 0.5932 (m-30) REVERT: F 172 LEU cc_start: 0.8074 (tp) cc_final: 0.7763 (tp) REVERT: F 180 LEU cc_start: 0.9040 (tt) cc_final: 0.8739 (mt) REVERT: F 183 PHE cc_start: 0.8529 (p90) cc_final: 0.8276 (p90) REVERT: F 243 TYR cc_start: 0.7837 (m-80) cc_final: 0.7428 (m-80) REVERT: F 254 PHE cc_start: 0.6604 (t80) cc_final: 0.6259 (t80) REVERT: F 266 PHE cc_start: 0.8705 (m-80) cc_final: 0.8192 (m-80) REVERT: F 278 MET cc_start: 0.5381 (mmm) cc_final: 0.3095 (mmm) REVERT: F 293 TYR cc_start: 0.7564 (p90) cc_final: 0.7210 (p90) REVERT: F 327 PHE cc_start: 0.8107 (m-80) cc_final: 0.7798 (m-80) REVERT: F 674 PHE cc_start: 0.8462 (m-80) cc_final: 0.8199 (m-10) REVERT: F 689 TYR cc_start: 0.8239 (p90) cc_final: 0.7996 (p90) REVERT: F 696 MET cc_start: 0.2328 (ptt) cc_final: 0.1941 (ptt) REVERT: D 18 VAL cc_start: 0.9623 (p) cc_final: 0.9367 (p) REVERT: D 80 MET cc_start: 0.5595 (ttm) cc_final: 0.4155 (ttm) REVERT: D 82 PHE cc_start: 0.9188 (m-80) cc_final: 0.8674 (m-10) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.1815 time to fit residues: 98.0843 Evaluate side-chains 260 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 221 optimal weight: 0.6980 chunk 104 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 251 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 842 GLN A1084 GLN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 81 GLN L 89 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1129 ASN E1132 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1084 GLN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.078663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.060377 restraints weight = 215959.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.061125 restraints weight = 187488.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.062360 restraints weight = 157515.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.062403 restraints weight = 131815.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.062736 restraints weight = 125278.141| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29433 Z= 0.170 Angle : 0.702 9.627 40143 Z= 0.360 Chirality : 0.046 0.491 4647 Planarity : 0.005 0.042 5061 Dihedral : 5.688 27.673 3873 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.64 % Favored : 94.10 % Rotamer: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -1.20 (0.14), residues: 3543 helix: -0.31 (0.18), residues: 684 sheet: -0.61 (0.18), residues: 747 loop : -1.01 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1069 TYR 0.026 0.002 TYR I 909 PHE 0.025 0.002 PHE B 266 TRP 0.055 0.003 TRP D 50 HIS 0.005 0.001 HIS A1146 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (29313) covalent geometry : angle 0.68381 / 0.36 (39825) SS BOND : bond 0.00422 / 0.26 ( 42) SS BOND : angle 0.99028 / 0.60 ( 84) hydrogen bonds : bond 0.04816 / 3.22 ( 1154) hydrogen bonds : angle 6.30651 / 4.52 ( 3024) link_ALPHA1-3 : bond 0.01133 / 0.52 ( 3) link_ALPHA1-3 : angle 1.20167 / 0.70 ( 9) link_ALPHA1-6 : bond 0.00431 / 0.20 ( 3) link_ALPHA1-6 : angle 1.50158 / 0.84 ( 9) link_BETA1-4 : bond 0.00346 / 0.23 ( 30) link_BETA1-4 : angle 1.73509 / 1.15 ( 90) link_NAG-ASN : bond 0.00429 / 0.27 ( 42) link_NAG-ASN : angle 2.50339 / 1.78 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.6307 (mmt) cc_final: 0.6099 (tpt) REVERT: A 906 MET cc_start: 0.1434 (ttm) cc_final: 0.1005 (tmm) REVERT: A 913 MET cc_start: 0.8348 (mpp) cc_final: 0.7769 (mpp) REVERT: A 921 ARG cc_start: 0.5594 (ttm170) cc_final: 0.4076 (pmt-80) REVERT: A 943 MET cc_start: 0.7711 (tpt) cc_final: 0.7277 (tpt) REVERT: A 1021 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8392 (mmtm) REVERT: A 1090 GLU cc_start: 0.8261 (mm-30) cc_final: 0.6774 (pp20) REVERT: B 108 ASP cc_start: 0.6176 (m-30) cc_final: 0.5830 (m-30) REVERT: B 148 MET cc_start: 0.9435 (tpt) cc_final: 0.9111 (tpp) REVERT: B 172 LEU cc_start: 0.7961 (tp) cc_final: 0.7620 (tp) REVERT: B 180 LEU cc_start: 0.8896 (tt) cc_final: 0.8621 (mt) REVERT: B 183 PHE cc_start: 0.8517 (p90) cc_final: 0.8143 (p90) REVERT: B 228 PHE cc_start: 0.9301 (t80) cc_final: 0.9037 (t80) REVERT: B 243 TYR cc_start: 0.7960 (m-80) cc_final: 0.7533 (m-80) REVERT: B 254 PHE cc_start: 0.6831 (t80) cc_final: 0.6603 (t80) REVERT: B 266 PHE cc_start: 0.9004 (m-80) cc_final: 0.8661 (m-80) REVERT: B 278 MET cc_start: 0.6043 (tpp) cc_final: 0.4886 (ttm) REVERT: B 293 TYR cc_start: 0.7289 (p90) cc_final: 0.6882 (p90) REVERT: B 327 PHE cc_start: 0.8246 (m-80) cc_final: 0.7896 (m-80) REVERT: B 674 PHE cc_start: 0.8493 (m-80) cc_final: 0.8228 (m-80) REVERT: B 689 TYR cc_start: 0.8244 (p90) cc_final: 0.7951 (p90) REVERT: B 696 MET cc_start: 0.2592 (ptt) cc_final: 0.2325 (ptt) REVERT: H 80 MET cc_start: 0.5959 (ttm) cc_final: 0.5255 (ttm) REVERT: E 757 MET cc_start: 0.5943 (mmt) cc_final: 0.5196 (mmt) REVERT: E 906 MET cc_start: 0.0990 (ttm) cc_final: 0.0547 (tmm) REVERT: E 913 MET cc_start: 0.8235 (mpp) cc_final: 0.7657 (mpp) REVERT: E 921 ARG cc_start: 0.5697 (ttm170) cc_final: 0.4070 (pmt-80) REVERT: E 955 ILE cc_start: 0.5182 (mm) cc_final: 0.4908 (mm) REVERT: E 1068 ASP cc_start: 0.5891 (t70) cc_final: 0.5622 (m-30) REVERT: E 1090 GLU cc_start: 0.8138 (mm-30) cc_final: 0.6674 (pp20) REVERT: E 1101 ASP cc_start: 0.8523 (m-30) cc_final: 0.8289 (t70) REVERT: E 1102 LYS cc_start: 0.9077 (mmpt) cc_final: 0.8702 (mmmt) REVERT: J 108 ASP cc_start: 0.6341 (m-30) cc_final: 0.6037 (m-30) REVERT: J 172 LEU cc_start: 0.7836 (tp) cc_final: 0.7599 (tp) REVERT: J 180 LEU cc_start: 0.8515 (pp) cc_final: 0.8060 (mt) REVERT: J 183 PHE cc_start: 0.8588 (p90) cc_final: 0.8188 (p90) REVERT: J 228 PHE cc_start: 0.9358 (t80) cc_final: 0.9139 (t80) REVERT: J 266 PHE cc_start: 0.8878 (m-80) cc_final: 0.8604 (m-80) REVERT: J 278 MET cc_start: 0.5564 (tpp) cc_final: 0.4148 (ttm) REVERT: J 327 PHE cc_start: 0.8250 (m-80) cc_final: 0.8004 (m-80) REVERT: J 606 TYR cc_start: 0.7706 (p90) cc_final: 0.7390 (p90) REVERT: J 632 TYR cc_start: 0.8756 (m-80) cc_final: 0.8461 (m-80) REVERT: J 674 PHE cc_start: 0.8338 (m-80) cc_final: 0.8077 (m-80) REVERT: C 80 MET cc_start: 0.6165 (ttm) cc_final: 0.4443 (ttm) REVERT: C 82 PHE cc_start: 0.9296 (m-80) cc_final: 0.8995 (m-10) REVERT: I 757 MET cc_start: 0.6435 (mtt) cc_final: 0.5733 (mmm) REVERT: I 809 TYR cc_start: 0.7352 (t80) cc_final: 0.7107 (t80) REVERT: I 921 ARG cc_start: 0.5737 (ttm170) cc_final: 0.3946 (pmt-80) REVERT: I 943 MET cc_start: 0.8047 (tpp) cc_final: 0.7470 (tpt) REVERT: I 1021 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8551 (mmtm) REVERT: I 1068 ASP cc_start: 0.6285 (t70) cc_final: 0.6007 (m-30) REVERT: I 1074 ARG cc_start: 0.7448 (mmt90) cc_final: 0.7183 (tpm170) REVERT: F 108 ASP cc_start: 0.6296 (m-30) cc_final: 0.6028 (m-30) REVERT: F 172 LEU cc_start: 0.8150 (tp) cc_final: 0.7810 (tp) REVERT: F 180 LEU cc_start: 0.9055 (tt) cc_final: 0.8766 (mt) REVERT: F 183 PHE cc_start: 0.8558 (p90) cc_final: 0.8193 (p90) REVERT: F 243 TYR cc_start: 0.7965 (m-80) cc_final: 0.7539 (m-80) REVERT: F 293 TYR cc_start: 0.7705 (p90) cc_final: 0.7096 (p90) REVERT: F 327 PHE cc_start: 0.8272 (m-80) cc_final: 0.7997 (m-80) REVERT: F 674 PHE cc_start: 0.8436 (m-80) cc_final: 0.8122 (m-80) REVERT: F 689 TYR cc_start: 0.8167 (p90) cc_final: 0.7951 (p90) REVERT: F 696 MET cc_start: 0.2483 (ptt) cc_final: 0.2079 (ptt) REVERT: D 18 VAL cc_start: 0.9585 (p) cc_final: 0.9173 (p) REVERT: D 80 MET cc_start: 0.6263 (ttm) cc_final: 0.4797 (ttm) outliers start: 1 outliers final: 0 residues processed: 332 average time/residue: 0.1834 time to fit residues: 99.5695 Evaluate side-chains 265 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 219 optimal weight: 6.9990 chunk 277 optimal weight: 8.9990 chunk 300 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 318 optimal weight: 7.9990 chunk 226 optimal weight: 40.0000 chunk 45 optimal weight: 0.8980 chunk 322 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 264 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN B 277 ASN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN L 89 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1132 ASN C 68 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.078089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.060255 restraints weight = 216581.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.060993 restraints weight = 187788.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.061262 restraints weight = 157804.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.061917 restraints weight = 143629.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.062484 restraints weight = 128185.727| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29433 Z= 0.177 Angle : 0.714 9.663 40143 Z= 0.365 Chirality : 0.047 0.522 4647 Planarity : 0.005 0.046 5061 Dihedral : 5.737 27.086 3873 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.69 % Favored : 93.06 % Rotamer: Outliers : 0.10 % Allowed : 1.58 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -1.29 (0.14), residues: 3543 helix: -0.27 (0.19), residues: 666 sheet: -0.72 (0.18), residues: 747 loop : -1.09 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 699 TYR 0.046 0.002 TYR A 909 PHE 0.041 0.002 PHE E 850 TRP 0.040 0.003 TRP D 50 HIS 0.005 0.001 HIS E1146 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (29313) covalent geometry : angle 0.69702 / 0.36 (39825) SS BOND : bond 0.00420 / 0.26 ( 42) SS BOND : angle 1.03729 / 0.71 ( 84) hydrogen bonds : bond 0.04806 / 3.21 ( 1154) hydrogen bonds : angle 6.39201 / 4.58 ( 3024) link_ALPHA1-3 : bond 0.01123 / 0.52 ( 3) link_ALPHA1-3 : angle 1.18175 / 0.69 ( 9) link_ALPHA1-6 : bond 0.00466 / 0.22 ( 3) link_ALPHA1-6 : angle 1.58236 / 0.88 ( 9) link_BETA1-4 : bond 0.00359 / 0.23 ( 30) link_BETA1-4 : angle 1.77615 / 1.19 ( 90) link_NAG-ASN : bond 0.00458 / 0.29 ( 42) link_NAG-ASN : angle 2.40989 / 1.73 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 333 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 833 GLN cc_start: 0.6952 (tp-100) cc_final: 0.6669 (tp-100) REVERT: A 906 MET cc_start: 0.1362 (ttm) cc_final: 0.0952 (tmm) REVERT: A 913 MET cc_start: 0.8461 (mpp) cc_final: 0.8142 (mpp) REVERT: A 921 ARG cc_start: 0.5570 (ttm170) cc_final: 0.4089 (pmt-80) REVERT: A 943 MET cc_start: 0.7752 (tpt) cc_final: 0.7287 (tpt) REVERT: A 955 ILE cc_start: 0.5445 (mm) cc_final: 0.5148 (mm) REVERT: A 1090 GLU cc_start: 0.8216 (mm-30) cc_final: 0.6621 (pp20) REVERT: A 1102 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8527 (mmmt) REVERT: B 108 ASP cc_start: 0.6169 (m-30) cc_final: 0.5799 (m-30) REVERT: B 156 PHE cc_start: 0.8133 (m-10) cc_final: 0.7924 (m-10) REVERT: B 172 LEU cc_start: 0.8097 (tp) cc_final: 0.7788 (tp) REVERT: B 180 LEU cc_start: 0.8891 (tt) cc_final: 0.8648 (mt) REVERT: B 183 PHE cc_start: 0.8394 (p90) cc_final: 0.7914 (p90) REVERT: B 228 PHE cc_start: 0.9302 (t80) cc_final: 0.9074 (t80) REVERT: B 243 TYR cc_start: 0.7928 (m-80) cc_final: 0.7497 (m-80) REVERT: B 266 PHE cc_start: 0.8918 (m-80) cc_final: 0.8567 (m-80) REVERT: B 278 MET cc_start: 0.6147 (tpp) cc_final: 0.5378 (ttm) REVERT: B 293 TYR cc_start: 0.7291 (p90) cc_final: 0.6841 (p90) REVERT: B 689 TYR cc_start: 0.8061 (p90) cc_final: 0.7819 (p90) REVERT: B 696 MET cc_start: 0.2939 (ptt) cc_final: 0.2567 (ptt) REVERT: H 80 MET cc_start: 0.5810 (ttm) cc_final: 0.5178 (ttm) REVERT: L 35 TRP cc_start: 0.7835 (m-90) cc_final: 0.7593 (m-90) REVERT: E 757 MET cc_start: 0.5956 (mmt) cc_final: 0.5281 (mmt) REVERT: E 906 MET cc_start: 0.0855 (ttm) cc_final: 0.0515 (tmm) REVERT: E 913 MET cc_start: 0.8429 (mpp) cc_final: 0.7999 (mpp) REVERT: E 921 ARG cc_start: 0.5833 (ttm170) cc_final: 0.4186 (pmt-80) REVERT: E 955 ILE cc_start: 0.5066 (mm) cc_final: 0.4795 (mm) REVERT: E 1074 ARG cc_start: 0.7417 (mmt90) cc_final: 0.7185 (tpm170) REVERT: E 1102 LYS cc_start: 0.9039 (mmpt) cc_final: 0.8832 (mmmt) REVERT: J 108 ASP cc_start: 0.6414 (m-30) cc_final: 0.6034 (m-30) REVERT: J 148 MET cc_start: 0.9285 (tpt) cc_final: 0.9011 (tpp) REVERT: J 161 MET cc_start: 0.2638 (mmp) cc_final: 0.2413 (mmm) REVERT: J 172 LEU cc_start: 0.7753 (tp) cc_final: 0.7511 (tp) REVERT: J 183 PHE cc_start: 0.8559 (p90) cc_final: 0.8081 (p90) REVERT: J 228 PHE cc_start: 0.9372 (t80) cc_final: 0.9099 (t80) REVERT: J 254 PHE cc_start: 0.6651 (t80) cc_final: 0.6171 (t80) REVERT: J 266 PHE cc_start: 0.8813 (m-80) cc_final: 0.8306 (m-80) REVERT: J 278 MET cc_start: 0.5529 (tpp) cc_final: 0.4039 (ttm) REVERT: J 606 TYR cc_start: 0.7636 (p90) cc_final: 0.7350 (p90) REVERT: J 632 TYR cc_start: 0.8752 (m-80) cc_final: 0.8463 (m-80) REVERT: J 674 PHE cc_start: 0.8367 (m-80) cc_final: 0.8072 (m-80) REVERT: J 686 MET cc_start: 0.4945 (mmp) cc_final: 0.4312 (mmm) REVERT: C 80 MET cc_start: 0.6576 (ttm) cc_final: 0.6238 (ttm) REVERT: C 100 MET cc_start: -0.0272 (mmp) cc_final: -0.0502 (mmp) REVERT: I 757 MET cc_start: 0.6562 (mtt) cc_final: 0.5545 (ppp) REVERT: I 809 TYR cc_start: 0.7409 (t80) cc_final: 0.7150 (t80) REVERT: I 921 ARG cc_start: 0.5920 (ttm170) cc_final: 0.4223 (pmt-80) REVERT: I 943 MET cc_start: 0.8098 (tpp) cc_final: 0.7846 (tpp) REVERT: I 955 ILE cc_start: 0.5247 (mm) cc_final: 0.5029 (mm) REVERT: I 1021 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8442 (mmtm) REVERT: I 1068 ASP cc_start: 0.6273 (t70) cc_final: 0.5960 (m-30) REVERT: I 1074 ARG cc_start: 0.7374 (mmt90) cc_final: 0.7153 (tpm170) REVERT: I 1102 LYS cc_start: 0.8884 (mmpt) cc_final: 0.8585 (mmmt) REVERT: F 108 ASP cc_start: 0.6412 (m-30) cc_final: 0.5933 (m-30) REVERT: F 172 LEU cc_start: 0.8138 (tp) cc_final: 0.7796 (tp) REVERT: F 180 LEU cc_start: 0.9033 (tt) cc_final: 0.8757 (mt) REVERT: F 183 PHE cc_start: 0.8519 (p90) cc_final: 0.8230 (p90) REVERT: F 226 ASN cc_start: 0.9534 (m-40) cc_final: 0.9303 (p0) REVERT: F 243 TYR cc_start: 0.7921 (m-80) cc_final: 0.7510 (m-80) REVERT: F 293 TYR cc_start: 0.7672 (p90) cc_final: 0.6958 (p90) REVERT: F 327 PHE cc_start: 0.8335 (m-80) cc_final: 0.8063 (m-80) REVERT: F 686 MET cc_start: 0.5068 (mmp) cc_final: 0.4675 (mmm) REVERT: F 696 MET cc_start: 0.2500 (ptt) cc_final: 0.2083 (ptt) REVERT: D 80 MET cc_start: 0.6493 (ttm) cc_final: 0.5744 (ttm) REVERT: D 82 PHE cc_start: 0.9354 (m-80) cc_final: 0.9100 (m-10) outliers start: 3 outliers final: 0 residues processed: 334 average time/residue: 0.1840 time to fit residues: 100.7691 Evaluate side-chains 264 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 333 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 345 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 280 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 150 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 81 GLN L 89 GLN L 90 GLN E 857 GLN ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN K 89 GLN K 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.078771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.060659 restraints weight = 218390.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.061619 restraints weight = 189088.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.062149 restraints weight = 157954.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.062477 restraints weight = 138849.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.062477 restraints weight = 129679.262| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29433 Z= 0.146 Angle : 0.679 9.639 40143 Z= 0.347 Chirality : 0.047 0.652 4647 Planarity : 0.005 0.045 5061 Dihedral : 5.529 27.494 3873 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.04 % Favored : 93.71 % Rotamer: Outliers : 0.10 % Allowed : 1.15 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -1.25 (0.14), residues: 3543 helix: -0.17 (0.19), residues: 669 sheet: -0.73 (0.18), residues: 747 loop : -1.07 (0.14), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1069 TYR 0.043 0.002 TYR B 632 PHE 0.029 0.002 PHE E 850 TRP 0.035 0.002 TRP D 50 HIS 0.003 0.001 HIS J 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (29313) covalent geometry : angle 0.66201 / 0.34 (39825) SS BOND : bond 0.00356 / 0.22 ( 42) SS BOND : angle 1.20232 / 0.75 ( 84) hydrogen bonds : bond 0.04509 / 3.05 ( 1154) hydrogen bonds : angle 6.23849 / 4.46 ( 3024) link_ALPHA1-3 : bond 0.01012 / 0.47 ( 3) link_ALPHA1-3 : angle 1.11098 / 0.64 ( 9) link_ALPHA1-6 : bond 0.00648 / 0.30 ( 3) link_ALPHA1-6 : angle 1.60318 / 0.89 ( 9) link_BETA1-4 : bond 0.00373 / 0.24 ( 30) link_BETA1-4 : angle 1.74757 / 1.15 ( 90) link_NAG-ASN : bond 0.00342 / 0.21 ( 42) link_NAG-ASN : angle 2.18690 / 1.57 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 346 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.6369 (tpt) cc_final: 0.5087 (tpt) REVERT: A 833 GLN cc_start: 0.6876 (tp-100) cc_final: 0.6551 (tp-100) REVERT: A 906 MET cc_start: 0.1115 (ttm) cc_final: 0.0747 (tmm) REVERT: A 913 MET cc_start: 0.8676 (mpp) cc_final: 0.8222 (mpp) REVERT: A 921 ARG cc_start: 0.5567 (ttm170) cc_final: 0.4121 (pmt-80) REVERT: A 943 MET cc_start: 0.7845 (tpt) cc_final: 0.7340 (tpt) REVERT: A 955 ILE cc_start: 0.5259 (mm) cc_final: 0.4976 (mm) REVERT: A 1090 GLU cc_start: 0.8298 (mm-30) cc_final: 0.6786 (pp20) REVERT: B 108 ASP cc_start: 0.6180 (m-30) cc_final: 0.5784 (m-30) REVERT: B 116 PHE cc_start: 0.6810 (p90) cc_final: 0.6559 (p90) REVERT: B 148 MET cc_start: 0.9428 (tpt) cc_final: 0.9172 (tpp) REVERT: B 172 LEU cc_start: 0.8073 (tp) cc_final: 0.7771 (tp) REVERT: B 183 PHE cc_start: 0.8365 (p90) cc_final: 0.7882 (p90) REVERT: B 228 PHE cc_start: 0.9302 (t80) cc_final: 0.9049 (t80) REVERT: B 243 TYR cc_start: 0.7977 (m-80) cc_final: 0.7445 (m-80) REVERT: B 266 PHE cc_start: 0.8894 (m-80) cc_final: 0.8559 (m-80) REVERT: B 278 MET cc_start: 0.6085 (tpp) cc_final: 0.5276 (ttm) REVERT: B 293 TYR cc_start: 0.7227 (p90) cc_final: 0.6665 (p90) REVERT: B 327 PHE cc_start: 0.8324 (m-80) cc_final: 0.8070 (m-80) REVERT: B 632 TYR cc_start: 0.8983 (m-80) cc_final: 0.8631 (m-80) REVERT: B 686 MET cc_start: 0.5193 (mmp) cc_final: 0.4977 (mmm) REVERT: B 689 TYR cc_start: 0.8087 (p90) cc_final: 0.7855 (p90) REVERT: B 696 MET cc_start: 0.2783 (ptt) cc_final: 0.2443 (ptt) REVERT: H 80 MET cc_start: 0.5665 (ttm) cc_final: 0.5128 (ttm) REVERT: H 100 MET cc_start: -0.1117 (mmp) cc_final: -0.1470 (mmp) REVERT: L 35 TRP cc_start: 0.7764 (m-90) cc_final: 0.7503 (m-90) REVERT: E 757 MET cc_start: 0.5877 (mmt) cc_final: 0.5109 (tpt) REVERT: E 906 MET cc_start: 0.0902 (ttm) cc_final: 0.0502 (tmm) REVERT: E 913 MET cc_start: 0.8702 (mpp) cc_final: 0.8166 (mpp) REVERT: E 921 ARG cc_start: 0.5811 (ttm170) cc_final: 0.4199 (pmt-80) REVERT: E 943 MET cc_start: 0.7548 (tpt) cc_final: 0.6782 (tpp) REVERT: E 955 ILE cc_start: 0.5107 (mm) cc_final: 0.4863 (mm) REVERT: E 1068 ASP cc_start: 0.6044 (t70) cc_final: 0.5734 (m-30) REVERT: E 1090 GLU cc_start: 0.8067 (mm-30) cc_final: 0.6602 (pp20) REVERT: E 1101 ASP cc_start: 0.8571 (m-30) cc_final: 0.8301 (t70) REVERT: E 1211 TYR cc_start: 0.8688 (m-10) cc_final: 0.8326 (m-80) REVERT: J 108 ASP cc_start: 0.6435 (m-30) cc_final: 0.5974 (m-30) REVERT: J 148 MET cc_start: 0.9358 (tpt) cc_final: 0.8985 (tpp) REVERT: J 161 MET cc_start: 0.3808 (mmp) cc_final: 0.3556 (mmm) REVERT: J 172 LEU cc_start: 0.7777 (tp) cc_final: 0.7541 (tp) REVERT: J 183 PHE cc_start: 0.8497 (p90) cc_final: 0.8022 (p90) REVERT: J 228 PHE cc_start: 0.9345 (t80) cc_final: 0.9079 (t80) REVERT: J 266 PHE cc_start: 0.8712 (m-80) cc_final: 0.8202 (m-80) REVERT: J 278 MET cc_start: 0.5546 (tpp) cc_final: 0.3835 (ttm) REVERT: J 293 TYR cc_start: 0.7584 (p90) cc_final: 0.7278 (p90) REVERT: J 315 VAL cc_start: 0.8610 (t) cc_final: 0.8307 (p) REVERT: J 606 TYR cc_start: 0.7582 (p90) cc_final: 0.7288 (p90) REVERT: J 632 TYR cc_start: 0.8711 (m-80) cc_final: 0.8492 (m-80) REVERT: J 674 PHE cc_start: 0.8446 (m-80) cc_final: 0.8165 (m-80) REVERT: J 686 MET cc_start: 0.5352 (mmp) cc_final: 0.4561 (mmm) REVERT: C 80 MET cc_start: 0.6562 (ttm) cc_final: 0.5174 (ttm) REVERT: C 82 PHE cc_start: 0.9381 (m-80) cc_final: 0.9111 (m-10) REVERT: I 757 MET cc_start: 0.6578 (mtt) cc_final: 0.5660 (ppp) REVERT: I 809 TYR cc_start: 0.7492 (t80) cc_final: 0.7237 (t80) REVERT: I 921 ARG cc_start: 0.5960 (ttm170) cc_final: 0.4331 (pmt-80) REVERT: I 943 MET cc_start: 0.8162 (tpp) cc_final: 0.7670 (tpt) REVERT: I 955 ILE cc_start: 0.5074 (mm) cc_final: 0.4850 (mm) REVERT: I 1021 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8443 (mmtm) REVERT: I 1068 ASP cc_start: 0.6368 (t70) cc_final: 0.6085 (m-30) REVERT: I 1090 GLU cc_start: 0.8225 (mm-30) cc_final: 0.6616 (pp20) REVERT: I 1211 TYR cc_start: 0.8710 (m-10) cc_final: 0.8262 (m-80) REVERT: F 108 ASP cc_start: 0.6428 (m-30) cc_final: 0.5815 (m-30) REVERT: F 172 LEU cc_start: 0.8115 (tp) cc_final: 0.7774 (tp) REVERT: F 180 LEU cc_start: 0.8999 (tt) cc_final: 0.8733 (mt) REVERT: F 183 PHE cc_start: 0.8501 (p90) cc_final: 0.8188 (p90) REVERT: F 226 ASN cc_start: 0.9496 (m-40) cc_final: 0.9245 (p0) REVERT: F 243 TYR cc_start: 0.7961 (m-80) cc_final: 0.7551 (m-80) REVERT: F 254 PHE cc_start: 0.6562 (t80) cc_final: 0.6269 (t80) REVERT: F 278 MET cc_start: 0.5080 (mmm) cc_final: 0.3049 (mmm) REVERT: F 293 TYR cc_start: 0.7623 (p90) cc_final: 0.7020 (p90) REVERT: F 327 PHE cc_start: 0.8345 (m-80) cc_final: 0.8039 (m-80) REVERT: F 674 PHE cc_start: 0.8707 (m-80) cc_final: 0.8425 (m-10) REVERT: F 686 MET cc_start: 0.5237 (mmp) cc_final: 0.4635 (mmm) REVERT: F 689 TYR cc_start: 0.8325 (p90) cc_final: 0.8030 (p90) REVERT: F 696 MET cc_start: 0.2535 (ptt) cc_final: 0.2122 (ptt) REVERT: D 59 TYR cc_start: 0.7111 (p90) cc_final: 0.6663 (p90) REVERT: D 82 PHE cc_start: 0.9314 (m-80) cc_final: 0.8884 (m-10) outliers start: 3 outliers final: 0 residues processed: 347 average time/residue: 0.1767 time to fit residues: 100.8063 Evaluate side-chains 270 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 66 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 253 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN A1132 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 81 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1104 ASN ** J 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 599 GLN ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 GLN ** F 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.075930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.058735 restraints weight = 230956.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.059370 restraints weight = 201414.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.059883 restraints weight = 168428.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.060201 restraints weight = 146541.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.060839 restraints weight = 134741.663| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.7295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 29433 Z= 0.268 Angle : 0.868 10.078 40143 Z= 0.446 Chirality : 0.052 0.808 4647 Planarity : 0.006 0.060 5061 Dihedral : 6.361 28.458 3873 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 29.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.07 % Favored : 91.67 % Rotamer: Outliers : 0.03 % Allowed : 1.22 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -1.75 (0.14), residues: 3543 helix: -0.92 (0.18), residues: 639 sheet: -0.95 (0.17), residues: 828 loop : -1.32 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 979 TYR 0.040 0.003 TYR B 632 PHE 0.027 0.003 PHE A1012 TRP 0.049 0.004 TRP C 50 HIS 0.010 0.002 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.27 (29313) covalent geometry : angle 0.84786 / 0.44 (39825) SS BOND : bond 0.00642 / 0.36 ( 42) SS BOND : angle 1.34407 / 0.85 ( 84) hydrogen bonds : bond 0.05665 / 3.75 ( 1154) hydrogen bonds : angle 7.10601 / 5.06 ( 3024) link_ALPHA1-3 : bond 0.00979 / 0.45 ( 3) link_ALPHA1-3 : angle 1.29648 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00497 / 0.23 ( 3) link_ALPHA1-6 : angle 1.95667 / 1.08 ( 9) link_BETA1-4 : bond 0.00382 / 0.25 ( 30) link_BETA1-4 : angle 2.22860 / 1.49 ( 90) link_NAG-ASN : bond 0.00781 / 0.49 ( 42) link_NAG-ASN : angle 2.76409 / 1.94 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.6481 (tpt) cc_final: 0.5025 (tpt) REVERT: A 842 GLN cc_start: 0.6519 (OUTLIER) cc_final: 0.6307 (tm-30) REVERT: A 906 MET cc_start: 0.1545 (ttm) cc_final: 0.1087 (tmm) REVERT: A 913 MET cc_start: 0.8823 (mpp) cc_final: 0.8306 (mpp) REVERT: A 921 ARG cc_start: 0.6390 (ttm170) cc_final: 0.4832 (pmt-80) REVERT: A 939 MET cc_start: 0.4648 (mpp) cc_final: 0.4312 (mmm) REVERT: A 943 MET cc_start: 0.7911 (tpt) cc_final: 0.7354 (tpt) REVERT: A 955 ILE cc_start: 0.5220 (mm) cc_final: 0.4946 (mm) REVERT: A 1102 LYS cc_start: 0.8839 (mmpt) cc_final: 0.8444 (mmmt) REVERT: B 108 ASP cc_start: 0.6378 (m-30) cc_final: 0.5987 (m-30) REVERT: B 116 PHE cc_start: 0.7302 (p90) cc_final: 0.7060 (p90) REVERT: B 183 PHE cc_start: 0.8440 (p90) cc_final: 0.8122 (p90) REVERT: B 228 PHE cc_start: 0.9334 (t80) cc_final: 0.9128 (t80) REVERT: B 243 TYR cc_start: 0.8128 (m-80) cc_final: 0.7529 (m-80) REVERT: B 278 MET cc_start: 0.6546 (tpp) cc_final: 0.6151 (ttm) REVERT: B 632 TYR cc_start: 0.9164 (m-80) cc_final: 0.8797 (m-80) REVERT: B 674 PHE cc_start: 0.8600 (m-80) cc_final: 0.8265 (m-10) REVERT: B 689 TYR cc_start: 0.8113 (p90) cc_final: 0.7849 (p90) REVERT: B 696 MET cc_start: 0.2603 (ptt) cc_final: 0.2062 (ptt) REVERT: H 80 MET cc_start: 0.5902 (ttm) cc_final: 0.5344 (ttm) REVERT: L 2 LEU cc_start: 0.7045 (mp) cc_final: 0.6795 (mp) REVERT: L 35 TRP cc_start: 0.7675 (m-90) cc_final: 0.7396 (m-90) REVERT: E 757 MET cc_start: 0.5998 (mmt) cc_final: 0.5295 (mmt) REVERT: E 906 MET cc_start: 0.0936 (ttm) cc_final: 0.0575 (tmm) REVERT: E 913 MET cc_start: 0.8646 (mpp) cc_final: 0.8103 (mpp) REVERT: E 921 ARG cc_start: 0.6221 (ttm170) cc_final: 0.4694 (pmt-80) REVERT: E 955 ILE cc_start: 0.5207 (mm) cc_final: 0.4876 (mm) REVERT: J 108 ASP cc_start: 0.6583 (m-30) cc_final: 0.6020 (m-30) REVERT: J 183 PHE cc_start: 0.8631 (p90) cc_final: 0.8222 (p90) REVERT: J 266 PHE cc_start: 0.8794 (m-80) cc_final: 0.8542 (m-80) REVERT: J 278 MET cc_start: 0.5509 (tpp) cc_final: 0.4915 (ttm) REVERT: J 293 TYR cc_start: 0.7563 (p90) cc_final: 0.7170 (p90) REVERT: J 606 TYR cc_start: 0.7791 (p90) cc_final: 0.7460 (p90) REVERT: J 674 PHE cc_start: 0.8340 (m-80) cc_final: 0.8043 (m-10) REVERT: C 100 MET cc_start: 0.1150 (mmp) cc_final: 0.0872 (mmp) REVERT: I 757 MET cc_start: 0.6777 (mtt) cc_final: 0.5820 (mtp) REVERT: I 809 TYR cc_start: 0.7812 (t80) cc_final: 0.7491 (t80) REVERT: I 921 ARG cc_start: 0.6611 (ttm170) cc_final: 0.5002 (pmt-80) REVERT: I 943 MET cc_start: 0.8136 (tpp) cc_final: 0.7575 (tpt) REVERT: I 955 ILE cc_start: 0.5224 (mm) cc_final: 0.4995 (mm) REVERT: I 1211 TYR cc_start: 0.8922 (m-10) cc_final: 0.8485 (m-80) REVERT: F 108 ASP cc_start: 0.6664 (m-30) cc_final: 0.6345 (m-30) REVERT: F 172 LEU cc_start: 0.8029 (tp) cc_final: 0.7699 (tp) REVERT: F 180 LEU cc_start: 0.9026 (tt) cc_final: 0.8822 (mt) REVERT: F 183 PHE cc_start: 0.8615 (p90) cc_final: 0.8255 (p90) REVERT: F 228 PHE cc_start: 0.9459 (t80) cc_final: 0.9259 (t80) REVERT: F 243 TYR cc_start: 0.8179 (m-80) cc_final: 0.7657 (m-80) REVERT: F 277 ASN cc_start: 0.7237 (m-40) cc_final: 0.6675 (m-40) REVERT: F 278 MET cc_start: 0.5822 (mmm) cc_final: 0.3720 (mtt) REVERT: F 327 PHE cc_start: 0.8370 (m-80) cc_final: 0.8167 (m-80) REVERT: F 674 PHE cc_start: 0.8675 (m-80) cc_final: 0.8442 (m-10) REVERT: F 689 TYR cc_start: 0.8325 (p90) cc_final: 0.8005 (p90) REVERT: D 80 MET cc_start: 0.6705 (ttm) cc_final: 0.5373 (ttm) REVERT: D 82 PHE cc_start: 0.9363 (m-80) cc_final: 0.9108 (m-10) REVERT: D 100 MET cc_start: -0.1301 (mmt) cc_final: -0.1549 (mmt) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.1840 time to fit residues: 91.0950 Evaluate side-chains 252 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 75 optimal weight: 3.9990 chunk 348 optimal weight: 30.0000 chunk 132 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 230 optimal weight: 40.0000 chunk 152 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 833 GLN A 836 HIS A 987 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 81 GLN L 6 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 987 GLN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.078067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.060455 restraints weight = 219655.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.061062 restraints weight = 191100.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.061601 restraints weight = 163262.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.061925 restraints weight = 142208.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.061925 restraints weight = 130015.198| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.7289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29433 Z= 0.161 Angle : 0.733 9.737 40143 Z= 0.375 Chirality : 0.048 0.622 4647 Planarity : 0.005 0.074 5061 Dihedral : 5.929 28.480 3873 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.58 % Favored : 93.17 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -1.52 (0.14), residues: 3543 helix: -0.60 (0.18), residues: 657 sheet: -0.76 (0.18), residues: 756 loop : -1.24 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 699 TYR 0.037 0.002 TYR B 632 PHE 0.031 0.002 PHE A1012 TRP 0.056 0.003 TRP C 50 HIS 0.011 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (29313) covalent geometry : angle 0.71448 / 0.37 (39825) SS BOND : bond 0.00351 / 0.22 ( 42) SS BOND : angle 1.20439 / 0.74 ( 84) hydrogen bonds : bond 0.04672 / 3.15 ( 1154) hydrogen bonds : angle 6.62013 / 4.72 ( 3024) link_ALPHA1-3 : bond 0.00955 / 0.44 ( 3) link_ALPHA1-3 : angle 1.12697 / 0.66 ( 9) link_ALPHA1-6 : bond 0.00883 / 0.40 ( 3) link_ALPHA1-6 : angle 1.85723 / 1.02 ( 9) link_BETA1-4 : bond 0.00355 / 0.23 ( 30) link_BETA1-4 : angle 1.97678 / 1.31 ( 90) link_NAG-ASN : bond 0.00374 / 0.23 ( 42) link_NAG-ASN : angle 2.38499 / 1.69 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.6236 (tpt) cc_final: 0.4866 (tpt) REVERT: A 833 GLN cc_start: 0.7255 (tp40) cc_final: 0.6909 (tp-100) REVERT: A 906 MET cc_start: 0.1315 (ttm) cc_final: 0.0921 (tmm) REVERT: A 913 MET cc_start: 0.8844 (mpp) cc_final: 0.8422 (mpp) REVERT: A 921 ARG cc_start: 0.6281 (ttm170) cc_final: 0.4785 (pmt-80) REVERT: A 939 MET cc_start: 0.5201 (mpp) cc_final: 0.4677 (mmm) REVERT: A 943 MET cc_start: 0.7974 (tpt) cc_final: 0.7504 (tpt) REVERT: A 955 ILE cc_start: 0.5360 (mm) cc_final: 0.5113 (mm) REVERT: A 1211 TYR cc_start: 0.8718 (m-10) cc_final: 0.8311 (m-80) REVERT: B 183 PHE cc_start: 0.8311 (p90) cc_final: 0.7901 (p90) REVERT: B 243 TYR cc_start: 0.8062 (m-80) cc_final: 0.7482 (m-80) REVERT: B 266 PHE cc_start: 0.8811 (m-80) cc_final: 0.8446 (m-80) REVERT: B 278 MET cc_start: 0.6388 (tpp) cc_final: 0.5676 (ttt) REVERT: B 293 TYR cc_start: 0.7231 (p90) cc_final: 0.6797 (p90) REVERT: B 315 VAL cc_start: 0.8366 (p) cc_final: 0.8159 (p) REVERT: B 327 PHE cc_start: 0.8488 (m-80) cc_final: 0.8257 (m-80) REVERT: B 632 TYR cc_start: 0.8981 (m-80) cc_final: 0.8731 (m-80) REVERT: B 674 PHE cc_start: 0.8495 (m-80) cc_final: 0.8182 (m-10) REVERT: B 689 TYR cc_start: 0.8072 (p90) cc_final: 0.7815 (p90) REVERT: B 696 MET cc_start: 0.2443 (ptt) cc_final: 0.1941 (ptt) REVERT: H 80 MET cc_start: 0.5987 (ttm) cc_final: 0.5483 (ttm) REVERT: L 35 TRP cc_start: 0.7733 (m-90) cc_final: 0.7482 (m-90) REVERT: E 757 MET cc_start: 0.5892 (mmt) cc_final: 0.5121 (tpt) REVERT: E 906 MET cc_start: 0.0934 (ttm) cc_final: 0.0533 (tmm) REVERT: E 913 MET cc_start: 0.8770 (mpp) cc_final: 0.8345 (mpp) REVERT: E 921 ARG cc_start: 0.6120 (ttm170) cc_final: 0.4665 (pmt-80) REVERT: J 108 ASP cc_start: 0.6422 (m-30) cc_final: 0.5703 (m-30) REVERT: J 148 MET cc_start: 0.9420 (tpt) cc_final: 0.9120 (tpp) REVERT: J 172 LEU cc_start: 0.7738 (tp) cc_final: 0.7513 (tp) REVERT: J 183 PHE cc_start: 0.8565 (p90) cc_final: 0.8120 (p90) REVERT: J 228 PHE cc_start: 0.9364 (t80) cc_final: 0.9051 (t80) REVERT: J 266 PHE cc_start: 0.8571 (m-80) cc_final: 0.8063 (m-80) REVERT: J 278 MET cc_start: 0.5923 (tpp) cc_final: 0.5264 (ttm) REVERT: J 315 VAL cc_start: 0.8568 (t) cc_final: 0.8078 (t) REVERT: J 327 PHE cc_start: 0.8546 (m-80) cc_final: 0.8305 (m-80) REVERT: J 606 TYR cc_start: 0.7670 (p90) cc_final: 0.7363 (p90) REVERT: J 674 PHE cc_start: 0.8273 (m-80) cc_final: 0.7937 (m-10) REVERT: J 686 MET cc_start: 0.5360 (mmm) cc_final: 0.4769 (mmm) REVERT: J 689 TYR cc_start: 0.8095 (p90) cc_final: 0.7870 (p90) REVERT: C 100 MET cc_start: 0.1060 (mmp) cc_final: 0.0791 (mmp) REVERT: I 757 MET cc_start: 0.6687 (mtt) cc_final: 0.5892 (mmt) REVERT: I 921 ARG cc_start: 0.6497 (ttm170) cc_final: 0.5035 (pmt-80) REVERT: I 943 MET cc_start: 0.8169 (tpp) cc_final: 0.7491 (tpt) REVERT: I 955 ILE cc_start: 0.5158 (mm) cc_final: 0.4943 (mm) REVERT: I 1211 TYR cc_start: 0.8895 (m-10) cc_final: 0.8521 (m-80) REVERT: F 108 ASP cc_start: 0.6217 (m-30) cc_final: 0.6008 (m-30) REVERT: F 172 LEU cc_start: 0.8200 (tp) cc_final: 0.7848 (tp) REVERT: F 180 LEU cc_start: 0.8942 (tt) cc_final: 0.8700 (mt) REVERT: F 183 PHE cc_start: 0.8518 (p90) cc_final: 0.8185 (p90) REVERT: F 226 ASN cc_start: 0.9527 (m-40) cc_final: 0.9221 (p0) REVERT: F 243 TYR cc_start: 0.8099 (m-80) cc_final: 0.7668 (m-80) REVERT: F 277 ASN cc_start: 0.7025 (m-40) cc_final: 0.6384 (m-40) REVERT: F 278 MET cc_start: 0.5672 (mmm) cc_final: 0.3018 (ttt) REVERT: F 293 TYR cc_start: 0.7608 (p90) cc_final: 0.7179 (p90) REVERT: F 327 PHE cc_start: 0.8409 (m-80) cc_final: 0.8091 (m-80) REVERT: F 674 PHE cc_start: 0.8594 (m-80) cc_final: 0.8308 (m-10) REVERT: F 686 MET cc_start: 0.5685 (mmm) cc_final: 0.5450 (mmm) REVERT: F 689 TYR cc_start: 0.8341 (p90) cc_final: 0.7999 (p90) REVERT: D 80 MET cc_start: 0.6714 (ttm) cc_final: 0.6098 (ttm) REVERT: D 100 MET cc_start: -0.1572 (mmt) cc_final: -0.1805 (mmp) outliers start: 1 outliers final: 0 residues processed: 332 average time/residue: 0.1784 time to fit residues: 97.6256 Evaluate side-chains 266 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 315 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 318 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 81 GLN L 6 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1132 ASN I1138 HIS ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** 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 = 0.4037 r_free = 0.4037 target = 0.077468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.059540 restraints weight = 220708.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.060207 restraints weight = 192737.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.060757 restraints weight = 165162.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.061213 restraints weight = 145778.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.061462 restraints weight = 133775.667| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29433 Z= 0.178 Angle : 0.738 9.694 40143 Z= 0.378 Chirality : 0.048 0.585 4647 Planarity : 0.005 0.051 5061 Dihedral : 5.958 28.847 3873 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.51 % Favored : 92.24 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -1.49 (0.14), residues: 3543 helix: -0.51 (0.18), residues: 657 sheet: -0.77 (0.18), residues: 756 loop : -1.23 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 979 TYR 0.036 0.002 TYR E 909 PHE 0.028 0.002 PHE C 82 TRP 0.051 0.003 TRP C 50 HIS 0.013 0.002 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (29313) covalent geometry : angle 0.72048 / 0.37 (39825) SS BOND : bond 0.00390 / 0.25 ( 42) SS BOND : angle 1.21856 / 0.78 ( 84) hydrogen bonds : bond 0.04723 / 3.16 ( 1154) hydrogen bonds : angle 6.67021 / 4.76 ( 3024) link_ALPHA1-3 : bond 0.00874 / 0.40 ( 3) link_ALPHA1-3 : angle 1.19495 / 0.70 ( 9) link_ALPHA1-6 : bond 0.00813 / 0.37 ( 3) link_ALPHA1-6 : angle 1.96414 / 1.07 ( 9) link_BETA1-4 : bond 0.00390 / 0.25 ( 30) link_BETA1-4 : angle 1.96543 / 1.29 ( 90) link_NAG-ASN : bond 0.00428 / 0.26 ( 42) link_NAG-ASN : angle 2.31231 / 1.62 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5236.44 seconds wall clock time: 91 minutes 57.82 seconds (5517.82 seconds total)