Starting phenix.real_space_refine on Mon Jul 28 20:27:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tyc_41713/07_2025/8tyc_41713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tyc_41713/07_2025/8tyc_41713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tyc_41713/07_2025/8tyc_41713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tyc_41713/07_2025/8tyc_41713.map" model { file = "/net/cci-nas-00/data/ceres_data/8tyc_41713/07_2025/8tyc_41713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tyc_41713/07_2025/8tyc_41713.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 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 93 5.16 5 C 6603 2.51 5 N 1712 2.21 5 O 2220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10628 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1536 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1583 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 195} Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1548 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "a" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1256 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain breaks: 1 Chain: "b" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1269 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "c" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1306 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.27, per 1000 atoms: 0.68 Number of scatterers: 10628 At special positions: 0 Unit cell: (111.622, 109.956, 109.123, 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 93 16.00 O 2220 8.00 N 1712 7.00 C 6603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.06 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.02 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.01 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.04 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.01 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.04 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.01 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 ALPHA1-2 " MAN Z 4 " - " MAN Z 5 " " MAN f 4 " - " MAN f 5 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA Z 3 " - " MAN Z 4 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 6 " " BMA f 3 " - " MAN f 6 " " BMA h 3 " - " MAN h 6 " BETA1-3 " NAG Q 1 " - " FUC Q 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " BETA1-6 " NAG W 1 " - " FUC W 3 " NAG-ASN " NAG C 301 " - " ASN C 99 " " NAG D 1 " - " ASN A 119 " " NAG E 1 " - " ASN A 79 " " NAG F 1 " - " ASN A 89 " " NAG G 1 " - " ASN A 99 " " NAG I 1 " - " ASN A 109 " " NAG J 1 " - " ASN A 167 " " NAG K 1 " - " ASN A 224 " " NAG M 1 " - " ASN B 99 " " NAG N 1 " - " ASN B 224 " " NAG O 1 " - " ASN B 167 " " NAG P 1 " - " ASN B 119 " " NAG Q 1 " - " ASN B 109 " " NAG R 1 " - " ASN B 89 " " NAG S 1 " - " ASN B 79 " " NAG T 1 " - " ASN C 119 " " NAG U 1 " - " ASN C 79 " " NAG V 1 " - " ASN C 89 " " NAG W 1 " - " ASN C 109 " " NAG X 1 " - " ASN C 167 " " NAG Y 1 " - " ASN C 224 " " NAG Z 1 " - " ASN a 365 " " NAG a 701 " - " ASN a 395 " " NAG a 702 " - " ASN a 390 " " NAG b 701 " - " ASN b 390 " " NAG c 701 " - " ASN c 395 " " NAG c 702 " - " ASN c 390 " " NAG d 1 " - " ASN a 373 " " NAG e 1 " - " ASN b 373 " " NAG f 1 " - " ASN b 365 " " NAG g 1 " - " ASN b 395 " " NAG h 1 " - " ASN c 365 " " NAG i 1 " - " ASN c 373 " Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 15 sheets defined 43.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.637A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.946A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 183 through 195 removed outlier: 4.124A pdb=" N GLN B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.194A pdb=" N MET C 80 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.637A pdb=" N ARG C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.948A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.562A pdb=" N UNK H 32 " --> pdb=" O UNK H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.528A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU a 344 " --> pdb=" O ALA a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 420 Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 334 through 345 removed outlier: 4.968A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 347 through 359 Processing helix chain 'b' and resid 399 through 420 Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 removed outlier: 3.559A pdb=" N GLN c 324 " --> pdb=" O LYS c 320 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.599A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.500A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 396 through 398 No H-bonds generated for 'chain 'c' and resid 396 through 398' Processing helix chain 'c' and resid 399 through 420 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.600A pdb=" N GLY A 102 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.541A pdb=" N GLY C 102 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.012A pdb=" N UNK H 45 " --> pdb=" O UNK H 39 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N UNK H 39 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N UNK H 47 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N UNK H 37 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N UNK H 49 " --> pdb=" O UNK H 35 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N UNK H 35 " --> pdb=" O UNK H 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 52 through 53 removed outlier: 4.346A pdb=" N UNK L 44 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N UNK L 37 " --> pdb=" O UNK L 44 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N UNK L 46 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N UNK L 35 " --> pdb=" O UNK L 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB5, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB6, first strand: chain 'c' and resid 388 through 389 425 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2494 1.33 - 1.47: 3481 1.47 - 1.61: 4690 1.61 - 1.75: 8 1.75 - 1.89: 139 Bond restraints: 10812 Sorted by residual: bond pdb=" CA SER C 121 " pdb=" CB SER C 121 " ideal model delta sigma weight residual 1.527 1.427 0.100 1.15e-02 7.56e+03 7.55e+01 bond pdb=" CB LEU B 259 " pdb=" CG LEU B 259 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" CB HIS A 115 " pdb=" CG HIS A 115 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.66e+01 bond pdb=" NE1 TRP b 386 " pdb=" CE2 TRP b 386 " ideal model delta sigma weight residual 1.370 1.309 0.061 1.10e-02 8.26e+03 3.10e+01 bond pdb=" CB LEU A 259 " pdb=" CG LEU A 259 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.96e+01 ... (remaining 10807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 13517 3.09 - 6.18: 1087 6.18 - 9.27: 68 9.27 - 12.36: 5 12.36 - 15.44: 2 Bond angle restraints: 14679 Sorted by residual: angle pdb=" N ILE b 350 " pdb=" CA ILE b 350 " pdb=" C ILE b 350 " ideal model delta sigma weight residual 111.58 101.80 9.78 1.06e+00 8.90e-01 8.51e+01 angle pdb=" N SER c 269 " pdb=" CA SER c 269 " pdb=" C SER c 269 " ideal model delta sigma weight residual 111.07 119.14 -8.07 1.07e+00 8.73e-01 5.69e+01 angle pdb=" C ALA c 328 " pdb=" N PRO c 329 " pdb=" CA PRO c 329 " ideal model delta sigma weight residual 120.31 127.42 -7.11 9.80e-01 1.04e+00 5.26e+01 angle pdb=" N LEU c 349 " pdb=" CA LEU c 349 " pdb=" C LEU c 349 " ideal model delta sigma weight residual 111.69 103.48 8.21 1.23e+00 6.61e-01 4.45e+01 angle pdb=" CA ASP a 357 " pdb=" CB ASP a 357 " pdb=" CG ASP a 357 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.37e+01 ... (remaining 14674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 7118 21.41 - 42.83: 207 42.83 - 64.24: 48 64.24 - 85.66: 72 85.66 - 107.07: 42 Dihedral angle restraints: 7487 sinusoidal: 3742 harmonic: 3745 Sorted by residual: dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS c 360 " pdb=" CB CYS c 360 " ideal model delta sinusoidal sigma weight residual -86.00 -141.13 55.13 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" CA CYS B 118 " pdb=" CB CYS B 118 " pdb=" SG CYS B 118 " pdb=" SG CYS B 155 " ideal model delta sinusoidal sigma weight residual 79.00 7.75 71.25 1 2.00e+01 2.50e-03 1.63e+01 dihedral pdb=" O4 BMA h 3 " pdb=" C4 BMA h 3 " pdb=" C5 BMA h 3 " pdb=" O5 BMA h 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.36 107.07 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 7484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1531 0.183 - 0.366: 289 0.366 - 0.549: 81 0.549 - 0.732: 1 0.732 - 0.915: 1 Chirality restraints: 1903 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.14e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.77e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.75e+02 ... (remaining 1900 not shown) Planarity restraints: 1795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.11e+03 pdb=" C7 NAG T 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.127 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 1 " -0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG g 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG g 1 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG g 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG g 1 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 2 " -0.312 2.00e-02 2.50e+03 2.63e-01 8.66e+02 pdb=" C7 NAG g 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG g 2 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG g 2 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG g 2 " -0.037 2.00e-02 2.50e+03 ... (remaining 1792 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3855 2.87 - 3.38: 10103 3.38 - 3.89: 17579 3.89 - 4.39: 21043 4.39 - 4.90: 32250 Nonbonded interactions: 84830 Sorted by model distance: nonbonded pdb=" O ALA A 195 " pdb=" O GLY A 197 " model vdw 2.365 3.040 nonbonded pdb=" N ASP C 122 " pdb=" N ALA C 123 " model vdw 2.367 2.560 nonbonded pdb=" OD2 ASP B 251 " pdb=" NZ LYS c 339 " model vdw 2.369 3.120 nonbonded pdb=" O SER C 121 " pdb=" OG SER C 121 " model vdw 2.376 3.040 nonbonded pdb=" N ASP B 251 " pdb=" OD1 ASP B 251 " model vdw 2.388 3.120 ... (remaining 84825 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 60 through 171 or resid 179 through 259)) selection = (chain 'C' and (resid 60 through 171 or resid 179 through 259)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) } ncs_group { reference = (chain 'H' and resid 4 through 111) selection = chain 'L' } ncs_group { reference = chain 'Z' selection = chain 'f' selection = chain 'h' } ncs_group { reference = (chain 'a' and (resid 260 through 420 or resid 701)) selection = (chain 'b' and (resid 260 through 268 or resid 276 through 420 or resid 701)) selection = (chain 'c' and (resid 260 through 268 or resid 276 through 420 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.900 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.022 0.133 10912 Z= 1.161 Angle : 1.834 15.444 14959 Z= 1.076 Chirality : 0.154 0.915 1903 Planarity : 0.016 0.297 1762 Dihedral : 16.239 107.073 4999 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1038 helix: -0.37 (0.25), residues: 365 sheet: 1.14 (0.48), residues: 111 loop : 0.79 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.010 TRP C 196 HIS 0.012 0.003 HIS a 354 PHE 0.025 0.004 PHE A 233 TYR 0.063 0.009 TYR C 253 ARG 0.006 0.001 ARG A 250 Details of bonding type rmsd link_NAG-ASN : bond 0.07425 ( 33) link_NAG-ASN : angle 3.03249 ( 99) link_ALPHA1-6 : bond 0.05101 ( 3) link_ALPHA1-6 : angle 2.88869 ( 9) link_BETA1-4 : bond 0.07150 ( 36) link_BETA1-4 : angle 5.51331 ( 108) link_ALPHA1-2 : bond 0.08386 ( 3) link_ALPHA1-2 : angle 5.00615 ( 9) link_ALPHA1-3 : bond 0.08120 ( 3) link_ALPHA1-3 : angle 4.58051 ( 9) hydrogen bonds : bond 0.18766 ( 425) hydrogen bonds : angle 7.37351 ( 1065) link_BETA1-6 : bond 0.04972 ( 1) link_BETA1-6 : angle 2.70987 ( 3) SS BOND : bond 0.01104 ( 20) SS BOND : angle 3.01158 ( 40) link_BETA1-3 : bond 0.10280 ( 1) link_BETA1-3 : angle 6.14907 ( 3) covalent geometry : bond 0.02115 (10812) covalent geometry : angle 1.75336 (14679) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.050 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: a 405 GLN cc_start: 0.8519 (tp40) cc_final: 0.7979 (tp-100) REVERT: a 409 ASN cc_start: 0.8895 (m-40) cc_final: 0.8623 (m-40) REVERT: c 406 GLN cc_start: 0.8649 (tp40) cc_final: 0.8215 (tp-100) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2767 time to fit residues: 118.0690 Evaluate side-chains 179 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 92 HIS B 165 GLN C 149 GLN C 179 HIS b 348 GLN b 409 ASN c 348 GLN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 409 ASN ** 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 = 0.3909 r_free = 0.3909 target = 0.110902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.086968 restraints weight = 26900.438| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 4.17 r_work: 0.3324 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10912 Z= 0.196 Angle : 0.956 19.710 14959 Z= 0.446 Chirality : 0.050 0.587 1903 Planarity : 0.004 0.040 1762 Dihedral : 13.136 85.034 2987 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.05 % Allowed : 10.20 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1038 helix: 0.91 (0.28), residues: 354 sheet: 2.36 (0.50), residues: 93 loop : 0.51 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 210 HIS 0.007 0.002 HIS A 141 PHE 0.018 0.002 PHE c 293 TYR 0.019 0.002 TYR A 94 ARG 0.004 0.001 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00803 ( 33) link_NAG-ASN : angle 3.15491 ( 99) link_ALPHA1-6 : bond 0.00847 ( 3) link_ALPHA1-6 : angle 1.69563 ( 9) link_BETA1-4 : bond 0.01320 ( 36) link_BETA1-4 : angle 3.94853 ( 108) link_ALPHA1-2 : bond 0.00546 ( 3) link_ALPHA1-2 : angle 2.39826 ( 9) link_ALPHA1-3 : bond 0.01666 ( 3) link_ALPHA1-3 : angle 1.35375 ( 9) hydrogen bonds : bond 0.05624 ( 425) hydrogen bonds : angle 5.70629 ( 1065) link_BETA1-6 : bond 0.00311 ( 1) link_BETA1-6 : angle 1.64855 ( 3) SS BOND : bond 0.00665 ( 20) SS BOND : angle 2.85124 ( 40) link_BETA1-3 : bond 0.01214 ( 1) link_BETA1-3 : angle 2.31578 ( 3) covalent geometry : bond 0.00415 (10812) covalent geometry : angle 0.84808 (14679) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.7943 (mmt) cc_final: 0.7662 (mmp) REVERT: B 100 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8327 (tm-30) REVERT: C 85 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8184 (p) REVERT: C 251 ASP cc_start: 0.8724 (m-30) cc_final: 0.8251 (m-30) REVERT: a 282 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7383 (tmm-80) REVERT: a 304 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8720 (mtpp) REVERT: a 405 GLN cc_start: 0.8805 (tp40) cc_final: 0.7628 (tp-100) REVERT: a 406 GLN cc_start: 0.9322 (tp40) cc_final: 0.9098 (tp-100) REVERT: a 409 ASN cc_start: 0.9064 (m-40) cc_final: 0.8856 (m-40) REVERT: b 287 GLU cc_start: 0.9189 (pt0) cc_final: 0.8842 (pp20) REVERT: b 295 ASN cc_start: 0.8305 (p0) cc_final: 0.7930 (t0) REVERT: b 384 LYS cc_start: 0.8358 (mptt) cc_final: 0.8101 (mptt) REVERT: b 406 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8378 (mm-40) REVERT: c 289 GLU cc_start: 0.8104 (mp0) cc_final: 0.7769 (pm20) REVERT: c 304 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8592 (mtmm) REVERT: c 371 TYR cc_start: 0.8509 (p90) cc_final: 0.8198 (p90) REVERT: c 406 GLN cc_start: 0.8631 (tp40) cc_final: 0.8168 (tp-100) REVERT: c 410 MET cc_start: 0.7455 (mmm) cc_final: 0.6931 (mmm) outliers start: 29 outliers final: 12 residues processed: 225 average time/residue: 0.2340 time to fit residues: 73.5641 Evaluate side-chains 193 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 282 ARG Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN c 354 HIS c 374 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.108784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.084639 restraints weight = 27670.169| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.24 r_work: 0.3288 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10912 Z= 0.186 Angle : 0.879 19.918 14959 Z= 0.410 Chirality : 0.049 0.548 1903 Planarity : 0.004 0.044 1762 Dihedral : 9.839 77.977 2987 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.26 % Allowed : 12.09 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1038 helix: 1.05 (0.28), residues: 361 sheet: 1.77 (0.48), residues: 116 loop : 0.09 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 210 HIS 0.006 0.001 HIS A 141 PHE 0.014 0.002 PHE c 293 TYR 0.020 0.002 TYR a 393 ARG 0.004 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 33) link_NAG-ASN : angle 2.85350 ( 99) link_ALPHA1-6 : bond 0.00754 ( 3) link_ALPHA1-6 : angle 1.69705 ( 9) link_BETA1-4 : bond 0.01163 ( 36) link_BETA1-4 : angle 3.18513 ( 108) link_ALPHA1-2 : bond 0.00264 ( 3) link_ALPHA1-2 : angle 1.97159 ( 9) link_ALPHA1-3 : bond 0.01315 ( 3) link_ALPHA1-3 : angle 0.84592 ( 9) hydrogen bonds : bond 0.04751 ( 425) hydrogen bonds : angle 5.20998 ( 1065) link_BETA1-6 : bond 0.00119 ( 1) link_BETA1-6 : angle 1.88699 ( 3) SS BOND : bond 0.01398 ( 20) SS BOND : angle 3.72793 ( 40) link_BETA1-3 : bond 0.01109 ( 1) link_BETA1-3 : angle 2.99939 ( 3) covalent geometry : bond 0.00402 (10812) covalent geometry : angle 0.78240 (14679) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7757 (mp0) REVERT: A 80 MET cc_start: 0.9022 (mmm) cc_final: 0.8744 (mmm) REVERT: A 211 ASP cc_start: 0.8043 (m-30) cc_final: 0.7585 (p0) REVERT: A 259 LEU cc_start: 0.7873 (tp) cc_final: 0.7590 (tt) REVERT: B 100 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8267 (tm-30) REVERT: B 192 MET cc_start: 0.9041 (tmm) cc_final: 0.8833 (tmm) REVERT: B 214 MET cc_start: 0.8648 (mtm) cc_final: 0.8418 (mtt) REVERT: C 251 ASP cc_start: 0.8822 (m-30) cc_final: 0.8356 (m-30) REVERT: a 308 GLU cc_start: 0.8213 (mp0) cc_final: 0.7544 (mt-10) REVERT: a 396 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7152 (tm-30) REVERT: a 405 GLN cc_start: 0.8518 (tp40) cc_final: 0.7976 (tp-100) REVERT: a 406 GLN cc_start: 0.9389 (tp40) cc_final: 0.9077 (tp40) REVERT: a 409 ASN cc_start: 0.9308 (m-40) cc_final: 0.8981 (m-40) REVERT: b 283 TRP cc_start: 0.7741 (m100) cc_final: 0.7472 (m100) REVERT: b 287 GLU cc_start: 0.9185 (pt0) cc_final: 0.8827 (pp20) REVERT: b 304 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8645 (mtpp) REVERT: b 327 LYS cc_start: 0.7972 (ptmt) cc_final: 0.7343 (pttt) REVERT: b 352 LYS cc_start: 0.8514 (tttm) cc_final: 0.8232 (tttt) REVERT: b 384 LYS cc_start: 0.8347 (mptt) cc_final: 0.8072 (mptt) REVERT: b 401 ASP cc_start: 0.9162 (t70) cc_final: 0.8911 (t0) REVERT: b 406 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8339 (mm-40) REVERT: c 284 MET cc_start: 0.8452 (mtt) cc_final: 0.8163 (mtp) REVERT: c 304 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8491 (mtpp) REVERT: c 308 GLU cc_start: 0.8239 (mp0) cc_final: 0.7919 (mp0) REVERT: c 312 MET cc_start: 0.8930 (mmm) cc_final: 0.8585 (mmp) REVERT: c 371 TYR cc_start: 0.8608 (p90) cc_final: 0.8133 (p90) REVERT: c 406 GLN cc_start: 0.8662 (tp40) cc_final: 0.8344 (tp-100) outliers start: 31 outliers final: 13 residues processed: 205 average time/residue: 0.2452 time to fit residues: 70.9829 Evaluate side-chains 195 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain a residue 282 ARG Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 305 HIS ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.106669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.082605 restraints weight = 27413.569| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 4.14 r_work: 0.3251 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10912 Z= 0.205 Angle : 0.877 25.341 14959 Z= 0.410 Chirality : 0.049 0.524 1903 Planarity : 0.003 0.045 1762 Dihedral : 8.552 70.569 2987 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.36 % Allowed : 12.51 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1038 helix: 1.00 (0.28), residues: 363 sheet: 1.55 (0.45), residues: 125 loop : -0.12 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 210 HIS 0.008 0.001 HIS C 141 PHE 0.010 0.001 PHE a 399 TYR 0.027 0.002 TYR c 366 ARG 0.004 0.001 ARG B 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 33) link_NAG-ASN : angle 2.68818 ( 99) link_ALPHA1-6 : bond 0.00817 ( 3) link_ALPHA1-6 : angle 1.75998 ( 9) link_BETA1-4 : bond 0.01011 ( 36) link_BETA1-4 : angle 2.94402 ( 108) link_ALPHA1-2 : bond 0.00251 ( 3) link_ALPHA1-2 : angle 2.08904 ( 9) link_ALPHA1-3 : bond 0.01240 ( 3) link_ALPHA1-3 : angle 1.13600 ( 9) hydrogen bonds : bond 0.04411 ( 425) hydrogen bonds : angle 5.09634 ( 1065) link_BETA1-6 : bond 0.00063 ( 1) link_BETA1-6 : angle 2.05154 ( 3) SS BOND : bond 0.00865 ( 20) SS BOND : angle 3.92558 ( 40) link_BETA1-3 : bond 0.01135 ( 1) link_BETA1-3 : angle 2.72858 ( 3) covalent geometry : bond 0.00458 (10812) covalent geometry : angle 0.78811 (14679) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7775 (mp0) REVERT: A 259 LEU cc_start: 0.7878 (tp) cc_final: 0.7589 (tt) REVERT: B 100 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 130 ASP cc_start: 0.8432 (t0) cc_final: 0.8189 (t0) REVERT: B 192 MET cc_start: 0.9037 (tmm) cc_final: 0.8820 (tmm) REVERT: C 251 ASP cc_start: 0.8897 (m-30) cc_final: 0.8490 (m-30) REVERT: a 304 LYS cc_start: 0.9380 (mtpp) cc_final: 0.9152 (mtpp) REVERT: a 308 GLU cc_start: 0.8307 (mp0) cc_final: 0.7699 (mt-10) REVERT: a 396 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7202 (tm-30) REVERT: a 406 GLN cc_start: 0.9403 (tp40) cc_final: 0.9039 (tp40) REVERT: a 410 MET cc_start: 0.7552 (mmm) cc_final: 0.7165 (mtp) REVERT: b 283 TRP cc_start: 0.7694 (m100) cc_final: 0.7422 (m100) REVERT: b 287 GLU cc_start: 0.9248 (pt0) cc_final: 0.8887 (pp20) REVERT: b 304 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8630 (mtpp) REVERT: b 306 ASP cc_start: 0.9008 (p0) cc_final: 0.8737 (p0) REVERT: b 327 LYS cc_start: 0.7883 (ptmt) cc_final: 0.7345 (pttt) REVERT: b 352 LYS cc_start: 0.8525 (tttm) cc_final: 0.8236 (tttt) REVERT: b 401 ASP cc_start: 0.9195 (t70) cc_final: 0.8791 (t0) REVERT: b 405 GLN cc_start: 0.9193 (pt0) cc_final: 0.8982 (pt0) REVERT: b 408 ASP cc_start: 0.9395 (t70) cc_final: 0.9067 (m-30) REVERT: c 312 MET cc_start: 0.8884 (mmm) cc_final: 0.8477 (mmp) REVERT: c 371 TYR cc_start: 0.8677 (p90) cc_final: 0.8240 (p90) REVERT: c 405 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8645 (tm-30) REVERT: c 406 GLN cc_start: 0.8741 (tp40) cc_final: 0.8221 (tp-100) REVERT: c 410 MET cc_start: 0.7255 (mmm) cc_final: 0.6650 (mmm) outliers start: 32 outliers final: 20 residues processed: 215 average time/residue: 0.2222 time to fit residues: 67.7097 Evaluate side-chains 199 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 120 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 405 GLN c 354 HIS c 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.108551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.084681 restraints weight = 27719.943| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.19 r_work: 0.3314 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10912 Z= 0.133 Angle : 0.827 23.041 14959 Z= 0.387 Chirality : 0.047 0.504 1903 Planarity : 0.003 0.046 1762 Dihedral : 7.904 62.294 2987 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.42 % Allowed : 15.04 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1038 helix: 1.18 (0.28), residues: 361 sheet: 1.29 (0.45), residues: 123 loop : -0.15 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 210 HIS 0.006 0.001 HIS A 93 PHE 0.010 0.001 PHE a 399 TYR 0.025 0.001 TYR c 366 ARG 0.003 0.000 ARG c 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 33) link_NAG-ASN : angle 2.48817 ( 99) link_ALPHA1-6 : bond 0.00952 ( 3) link_ALPHA1-6 : angle 1.75769 ( 9) link_BETA1-4 : bond 0.00976 ( 36) link_BETA1-4 : angle 2.71206 ( 108) link_ALPHA1-2 : bond 0.00216 ( 3) link_ALPHA1-2 : angle 1.98522 ( 9) link_ALPHA1-3 : bond 0.01274 ( 3) link_ALPHA1-3 : angle 0.99658 ( 9) hydrogen bonds : bond 0.03906 ( 425) hydrogen bonds : angle 4.93060 ( 1065) link_BETA1-6 : bond 0.00283 ( 1) link_BETA1-6 : angle 1.60351 ( 3) SS BOND : bond 0.00862 ( 20) SS BOND : angle 4.11939 ( 40) link_BETA1-3 : bond 0.01182 ( 1) link_BETA1-3 : angle 2.83310 ( 3) covalent geometry : bond 0.00269 (10812) covalent geometry : angle 0.74012 (14679) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7702 (mp0) REVERT: A 259 LEU cc_start: 0.7822 (tp) cc_final: 0.7548 (tt) REVERT: B 100 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 130 ASP cc_start: 0.8388 (t0) cc_final: 0.8102 (t0) REVERT: C 233 PHE cc_start: 0.8434 (t80) cc_final: 0.8135 (t80) REVERT: C 251 ASP cc_start: 0.8822 (m-30) cc_final: 0.8359 (m-30) REVERT: a 308 GLU cc_start: 0.8238 (mp0) cc_final: 0.7666 (mt-10) REVERT: a 396 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7302 (tm-30) REVERT: a 406 GLN cc_start: 0.9401 (tp40) cc_final: 0.8958 (tp40) REVERT: a 410 MET cc_start: 0.7692 (mmm) cc_final: 0.7279 (mtp) REVERT: b 283 TRP cc_start: 0.7573 (m100) cc_final: 0.7284 (m100) REVERT: b 287 GLU cc_start: 0.9227 (pt0) cc_final: 0.8898 (pp20) REVERT: b 289 GLU cc_start: 0.7623 (mp0) cc_final: 0.7253 (mp0) REVERT: b 295 ASN cc_start: 0.8334 (p0) cc_final: 0.8124 (m-40) REVERT: b 327 LYS cc_start: 0.7890 (ptmt) cc_final: 0.7389 (pttt) REVERT: b 352 LYS cc_start: 0.8531 (tttm) cc_final: 0.8237 (tttt) REVERT: b 401 ASP cc_start: 0.9139 (t70) cc_final: 0.8793 (t0) REVERT: b 406 GLN cc_start: 0.8480 (mm-40) cc_final: 0.7981 (mt0) REVERT: c 304 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8615 (mtmm) REVERT: c 308 GLU cc_start: 0.8242 (mp0) cc_final: 0.8008 (mp0) REVERT: c 312 MET cc_start: 0.8944 (mmm) cc_final: 0.8582 (mmt) REVERT: c 371 TYR cc_start: 0.8652 (p90) cc_final: 0.8252 (p90) REVERT: c 405 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8590 (tm-30) REVERT: c 406 GLN cc_start: 0.8715 (tp40) cc_final: 0.8396 (tp40) REVERT: c 410 MET cc_start: 0.7521 (mmm) cc_final: 0.6952 (mmm) outliers start: 23 outliers final: 16 residues processed: 222 average time/residue: 0.2257 time to fit residues: 71.2824 Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 392 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN ** b 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 335 GLN c 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.105509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.082240 restraints weight = 27826.222| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 4.06 r_work: 0.3263 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10912 Z= 0.203 Angle : 0.877 19.334 14959 Z= 0.410 Chirality : 0.049 0.529 1903 Planarity : 0.003 0.046 1762 Dihedral : 7.798 58.653 2987 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.89 % Allowed : 14.30 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1038 helix: 1.10 (0.28), residues: 358 sheet: 1.43 (0.45), residues: 121 loop : -0.18 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 210 HIS 0.008 0.001 HIS C 141 PHE 0.011 0.001 PHE a 399 TYR 0.018 0.002 TYR c 366 ARG 0.005 0.001 ARG c 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 33) link_NAG-ASN : angle 2.61345 ( 99) link_ALPHA1-6 : bond 0.00945 ( 3) link_ALPHA1-6 : angle 1.65553 ( 9) link_BETA1-4 : bond 0.00954 ( 36) link_BETA1-4 : angle 2.75628 ( 108) link_ALPHA1-2 : bond 0.00310 ( 3) link_ALPHA1-2 : angle 2.16638 ( 9) link_ALPHA1-3 : bond 0.01245 ( 3) link_ALPHA1-3 : angle 1.19449 ( 9) hydrogen bonds : bond 0.04278 ( 425) hydrogen bonds : angle 5.02729 ( 1065) link_BETA1-6 : bond 0.00142 ( 1) link_BETA1-6 : angle 2.18489 ( 3) SS BOND : bond 0.00965 ( 20) SS BOND : angle 4.25409 ( 40) link_BETA1-3 : bond 0.01127 ( 1) link_BETA1-3 : angle 2.75183 ( 3) covalent geometry : bond 0.00450 (10812) covalent geometry : angle 0.79073 (14679) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8344 (tp30) cc_final: 0.7733 (tm-30) REVERT: A 76 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7832 (mp0) REVERT: A 259 LEU cc_start: 0.7842 (tp) cc_final: 0.7404 (tt) REVERT: B 100 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8245 (tm-30) REVERT: B 130 ASP cc_start: 0.8512 (t0) cc_final: 0.8227 (t0) REVERT: B 214 MET cc_start: 0.8639 (mtm) cc_final: 0.8344 (ttt) REVERT: C 66 TYR cc_start: 0.8270 (m-80) cc_final: 0.8036 (m-80) REVERT: C 233 PHE cc_start: 0.8436 (t80) cc_final: 0.8117 (t80) REVERT: C 251 ASP cc_start: 0.8854 (m-30) cc_final: 0.8508 (m-30) REVERT: a 308 GLU cc_start: 0.8307 (mp0) cc_final: 0.7871 (mt-10) REVERT: a 366 TYR cc_start: 0.8581 (m-80) cc_final: 0.8320 (m-10) REVERT: a 396 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7379 (tm-30) REVERT: a 406 GLN cc_start: 0.9437 (tp40) cc_final: 0.8987 (tp40) REVERT: a 410 MET cc_start: 0.7819 (mmm) cc_final: 0.7424 (mtp) REVERT: b 283 TRP cc_start: 0.7651 (m100) cc_final: 0.7342 (m100) REVERT: b 287 GLU cc_start: 0.9250 (pt0) cc_final: 0.8908 (pp20) REVERT: b 289 GLU cc_start: 0.7756 (mp0) cc_final: 0.7316 (mp0) REVERT: b 311 ASP cc_start: 0.9120 (m-30) cc_final: 0.8638 (t0) REVERT: b 327 LYS cc_start: 0.7892 (ptmt) cc_final: 0.7354 (pttt) REVERT: b 384 LYS cc_start: 0.8549 (mttm) cc_final: 0.8303 (mttm) REVERT: b 401 ASP cc_start: 0.9142 (t70) cc_final: 0.8804 (t0) REVERT: c 304 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8673 (mtpp) REVERT: c 308 GLU cc_start: 0.8341 (mp0) cc_final: 0.7576 (mt-10) REVERT: c 312 MET cc_start: 0.8952 (mmm) cc_final: 0.8502 (mmp) REVERT: c 405 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8658 (tm-30) REVERT: c 406 GLN cc_start: 0.8736 (tp40) cc_final: 0.8193 (tp-100) REVERT: c 410 MET cc_start: 0.7573 (mmm) cc_final: 0.6911 (mmm) outliers start: 37 outliers final: 24 residues processed: 220 average time/residue: 0.3725 time to fit residues: 118.1550 Evaluate side-chains 206 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 312 MET Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 313 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 52 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 89 optimal weight: 0.0980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 409 ASN c 305 HIS c 374 HIS c 406 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.106447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082928 restraints weight = 28076.373| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.13 r_work: 0.3279 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10912 Z= 0.159 Angle : 0.837 18.166 14959 Z= 0.394 Chirality : 0.048 0.504 1903 Planarity : 0.003 0.047 1762 Dihedral : 7.444 59.379 2987 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.05 % Allowed : 16.19 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1038 helix: 1.16 (0.29), residues: 357 sheet: 1.36 (0.45), residues: 129 loop : -0.18 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 210 HIS 0.007 0.001 HIS A 93 PHE 0.011 0.001 PHE c 399 TYR 0.020 0.001 TYR c 366 ARG 0.005 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 33) link_NAG-ASN : angle 2.41163 ( 99) link_ALPHA1-6 : bond 0.01023 ( 3) link_ALPHA1-6 : angle 1.56100 ( 9) link_BETA1-4 : bond 0.00954 ( 36) link_BETA1-4 : angle 2.61428 ( 108) link_ALPHA1-2 : bond 0.00210 ( 3) link_ALPHA1-2 : angle 2.07852 ( 9) link_ALPHA1-3 : bond 0.01237 ( 3) link_ALPHA1-3 : angle 1.07824 ( 9) hydrogen bonds : bond 0.03992 ( 425) hydrogen bonds : angle 4.96022 ( 1065) link_BETA1-6 : bond 0.00080 ( 1) link_BETA1-6 : angle 1.75817 ( 3) SS BOND : bond 0.00931 ( 20) SS BOND : angle 4.31978 ( 40) link_BETA1-3 : bond 0.01222 ( 1) link_BETA1-3 : angle 2.86904 ( 3) covalent geometry : bond 0.00347 (10812) covalent geometry : angle 0.75308 (14679) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8297 (tp30) cc_final: 0.7678 (tm-30) REVERT: A 76 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7779 (mp0) REVERT: A 259 LEU cc_start: 0.7855 (tp) cc_final: 0.7452 (tt) REVERT: B 100 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8253 (tm-30) REVERT: B 130 ASP cc_start: 0.8481 (t0) cc_final: 0.8184 (t0) REVERT: B 214 MET cc_start: 0.8636 (mtm) cc_final: 0.8340 (ttt) REVERT: C 233 PHE cc_start: 0.8486 (t80) cc_final: 0.8133 (t80) REVERT: C 251 ASP cc_start: 0.8852 (m-30) cc_final: 0.8535 (m-30) REVERT: a 308 GLU cc_start: 0.8265 (mp0) cc_final: 0.7849 (mt-10) REVERT: a 366 TYR cc_start: 0.8526 (m-80) cc_final: 0.8221 (m-10) REVERT: a 396 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7359 (tm-30) REVERT: a 406 GLN cc_start: 0.9452 (tp40) cc_final: 0.9083 (tp40) REVERT: b 283 TRP cc_start: 0.7493 (m100) cc_final: 0.7183 (m100) REVERT: b 287 GLU cc_start: 0.9277 (pt0) cc_final: 0.8925 (pp20) REVERT: b 289 GLU cc_start: 0.7793 (mp0) cc_final: 0.7353 (mp0) REVERT: b 311 ASP cc_start: 0.9135 (m-30) cc_final: 0.8654 (t0) REVERT: b 384 LYS cc_start: 0.8588 (mttm) cc_final: 0.8337 (mttm) REVERT: b 401 ASP cc_start: 0.9194 (t70) cc_final: 0.8872 (t0) REVERT: c 304 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8624 (mtmm) REVERT: c 308 GLU cc_start: 0.8272 (mp0) cc_final: 0.7566 (mt-10) REVERT: c 312 MET cc_start: 0.8952 (mmm) cc_final: 0.8481 (mmp) REVERT: c 405 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8504 (tm-30) REVERT: c 406 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8259 (tp-100) REVERT: c 410 MET cc_start: 0.7614 (mmm) cc_final: 0.6906 (mmm) outliers start: 29 outliers final: 21 residues processed: 214 average time/residue: 0.3219 time to fit residues: 98.6689 Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 312 MET Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 313 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN b 406 GLN c 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.105641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.082418 restraints weight = 27737.156| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 4.07 r_work: 0.3268 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10912 Z= 0.177 Angle : 0.865 19.221 14959 Z= 0.405 Chirality : 0.048 0.506 1903 Planarity : 0.003 0.046 1762 Dihedral : 7.307 58.608 2987 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.26 % Allowed : 16.19 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1038 helix: 1.12 (0.29), residues: 356 sheet: 1.45 (0.46), residues: 127 loop : -0.21 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 210 HIS 0.007 0.001 HIS A 93 PHE 0.010 0.001 PHE a 399 TYR 0.024 0.001 TYR c 366 ARG 0.008 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 33) link_NAG-ASN : angle 2.44367 ( 99) link_ALPHA1-6 : bond 0.01051 ( 3) link_ALPHA1-6 : angle 1.48400 ( 9) link_BETA1-4 : bond 0.00972 ( 36) link_BETA1-4 : angle 2.62586 ( 108) link_ALPHA1-2 : bond 0.00281 ( 3) link_ALPHA1-2 : angle 2.12055 ( 9) link_ALPHA1-3 : bond 0.01267 ( 3) link_ALPHA1-3 : angle 1.15781 ( 9) hydrogen bonds : bond 0.04101 ( 425) hydrogen bonds : angle 4.93306 ( 1065) link_BETA1-6 : bond 0.00024 ( 1) link_BETA1-6 : angle 1.94139 ( 3) SS BOND : bond 0.00946 ( 20) SS BOND : angle 4.32505 ( 40) link_BETA1-3 : bond 0.01175 ( 1) link_BETA1-3 : angle 2.86412 ( 3) covalent geometry : bond 0.00390 (10812) covalent geometry : angle 0.78275 (14679) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8308 (tp30) cc_final: 0.7691 (tm-30) REVERT: A 76 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7805 (mp0) REVERT: A 259 LEU cc_start: 0.7821 (tp) cc_final: 0.7377 (tt) REVERT: B 75 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8085 (mtt) REVERT: B 100 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8242 (tm-30) REVERT: B 130 ASP cc_start: 0.8497 (t0) cc_final: 0.8194 (t0) REVERT: B 192 MET cc_start: 0.9203 (tmm) cc_final: 0.8846 (tmm) REVERT: B 214 MET cc_start: 0.8638 (mtm) cc_final: 0.8341 (ttt) REVERT: B 250 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7880 (tmm-80) REVERT: C 233 PHE cc_start: 0.8482 (t80) cc_final: 0.8183 (t80) REVERT: C 251 ASP cc_start: 0.8816 (m-30) cc_final: 0.8566 (m-30) REVERT: a 308 GLU cc_start: 0.8296 (mp0) cc_final: 0.7873 (mt-10) REVERT: a 366 TYR cc_start: 0.8571 (m-80) cc_final: 0.8316 (m-10) REVERT: a 396 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7332 (tm-30) REVERT: a 406 GLN cc_start: 0.9410 (tp40) cc_final: 0.9185 (tp40) REVERT: a 410 MET cc_start: 0.7475 (mtp) cc_final: 0.7230 (mtp) REVERT: b 283 TRP cc_start: 0.7490 (m100) cc_final: 0.7183 (m100) REVERT: b 287 GLU cc_start: 0.9274 (pt0) cc_final: 0.8943 (pp20) REVERT: b 289 GLU cc_start: 0.7811 (mp0) cc_final: 0.7347 (mp0) REVERT: b 311 ASP cc_start: 0.9132 (m-30) cc_final: 0.8675 (t0) REVERT: b 401 ASP cc_start: 0.9172 (t70) cc_final: 0.8836 (t0) REVERT: b 406 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: c 304 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8636 (mtmm) REVERT: c 308 GLU cc_start: 0.8276 (mp0) cc_final: 0.7559 (mt-10) REVERT: c 405 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8506 (tm-30) REVERT: c 406 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8386 (tp-100) outliers start: 31 outliers final: 23 residues processed: 208 average time/residue: 0.2377 time to fit residues: 70.1285 Evaluate side-chains 207 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 312 MET Chi-restraints excluded: chain b residue 406 GLN Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 122 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 GLN c 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.106240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.083130 restraints weight = 27799.963| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 4.05 r_work: 0.3285 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10912 Z= 0.155 Angle : 0.877 20.965 14959 Z= 0.412 Chirality : 0.048 0.492 1903 Planarity : 0.003 0.047 1762 Dihedral : 7.125 59.888 2987 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.94 % Allowed : 16.40 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1038 helix: 1.18 (0.29), residues: 354 sheet: 1.49 (0.46), residues: 127 loop : -0.15 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 210 HIS 0.005 0.001 HIS A 93 PHE 0.010 0.001 PHE a 262 TYR 0.022 0.001 TYR c 366 ARG 0.009 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 33) link_NAG-ASN : angle 2.36600 ( 99) link_ALPHA1-6 : bond 0.01086 ( 3) link_ALPHA1-6 : angle 1.43391 ( 9) link_BETA1-4 : bond 0.00969 ( 36) link_BETA1-4 : angle 2.56692 ( 108) link_ALPHA1-2 : bond 0.00237 ( 3) link_ALPHA1-2 : angle 2.09521 ( 9) link_ALPHA1-3 : bond 0.01283 ( 3) link_ALPHA1-3 : angle 1.13552 ( 9) hydrogen bonds : bond 0.04053 ( 425) hydrogen bonds : angle 4.88833 ( 1065) link_BETA1-6 : bond 0.00151 ( 1) link_BETA1-6 : angle 1.74216 ( 3) SS BOND : bond 0.00977 ( 20) SS BOND : angle 4.44162 ( 40) link_BETA1-3 : bond 0.01175 ( 1) link_BETA1-3 : angle 2.88639 ( 3) covalent geometry : bond 0.00337 (10812) covalent geometry : angle 0.79792 (14679) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8283 (tp30) cc_final: 0.7671 (tm-30) REVERT: A 76 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7770 (mp0) REVERT: A 259 LEU cc_start: 0.7795 (tp) cc_final: 0.7353 (tt) REVERT: B 70 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8561 (t) REVERT: B 75 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8071 (mtt) REVERT: B 100 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 130 ASP cc_start: 0.8477 (t0) cc_final: 0.8170 (t0) REVERT: B 192 MET cc_start: 0.9191 (tmm) cc_final: 0.8831 (tmm) REVERT: B 214 MET cc_start: 0.8615 (mtm) cc_final: 0.8311 (ttt) REVERT: B 250 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7852 (tmm-80) REVERT: C 75 MET cc_start: 0.8186 (ttp) cc_final: 0.7877 (ttp) REVERT: C 233 PHE cc_start: 0.8494 (t80) cc_final: 0.8100 (t80) REVERT: C 251 ASP cc_start: 0.8814 (m-30) cc_final: 0.8562 (m-30) REVERT: a 308 GLU cc_start: 0.8249 (mp0) cc_final: 0.7820 (mt-10) REVERT: a 366 TYR cc_start: 0.8584 (m-80) cc_final: 0.8169 (m-10) REVERT: a 396 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7238 (tm-30) REVERT: a 406 GLN cc_start: 0.9437 (tp40) cc_final: 0.9193 (tp40) REVERT: a 410 MET cc_start: 0.7475 (mtp) cc_final: 0.7236 (mtp) REVERT: b 283 TRP cc_start: 0.7436 (m100) cc_final: 0.7139 (m100) REVERT: b 287 GLU cc_start: 0.9275 (pt0) cc_final: 0.8950 (pp20) REVERT: b 289 GLU cc_start: 0.7788 (mp0) cc_final: 0.7287 (mp0) REVERT: b 311 ASP cc_start: 0.9118 (m-30) cc_final: 0.8647 (t0) REVERT: b 339 LYS cc_start: 0.8366 (mptt) cc_final: 0.8141 (mmtm) REVERT: b 401 ASP cc_start: 0.9182 (t70) cc_final: 0.8866 (t0) REVERT: c 304 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8593 (mtmm) REVERT: c 308 GLU cc_start: 0.8266 (mp0) cc_final: 0.7978 (mt-10) REVERT: c 405 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8549 (tm-30) REVERT: c 406 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8229 (tp-100) REVERT: c 410 MET cc_start: 0.7216 (mmt) cc_final: 0.6378 (mmm) outliers start: 28 outliers final: 21 residues processed: 208 average time/residue: 0.2827 time to fit residues: 84.6519 Evaluate side-chains 205 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 312 MET Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 121 optimal weight: 0.0070 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN c 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.104800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.081498 restraints weight = 28001.307| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.04 r_work: 0.3249 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 10912 Z= 0.225 Angle : 0.932 20.689 14959 Z= 0.440 Chirality : 0.050 0.509 1903 Planarity : 0.003 0.046 1762 Dihedral : 7.319 59.908 2987 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.94 % Allowed : 17.03 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1038 helix: 1.00 (0.28), residues: 356 sheet: 1.37 (0.46), residues: 129 loop : -0.23 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 210 HIS 0.008 0.001 HIS A 93 PHE 0.014 0.002 PHE c 399 TYR 0.023 0.001 TYR c 366 ARG 0.006 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 33) link_NAG-ASN : angle 2.51196 ( 99) link_ALPHA1-6 : bond 0.01092 ( 3) link_ALPHA1-6 : angle 1.29274 ( 9) link_BETA1-4 : bond 0.00955 ( 36) link_BETA1-4 : angle 2.64620 ( 108) link_ALPHA1-2 : bond 0.00293 ( 3) link_ALPHA1-2 : angle 2.18053 ( 9) link_ALPHA1-3 : bond 0.01198 ( 3) link_ALPHA1-3 : angle 1.23822 ( 9) hydrogen bonds : bond 0.04504 ( 425) hydrogen bonds : angle 5.03499 ( 1065) link_BETA1-6 : bond 0.00156 ( 1) link_BETA1-6 : angle 2.16967 ( 3) SS BOND : bond 0.01025 ( 20) SS BOND : angle 4.60259 ( 40) link_BETA1-3 : bond 0.01278 ( 1) link_BETA1-3 : angle 2.77225 ( 3) covalent geometry : bond 0.00516 (10812) covalent geometry : angle 0.85210 (14679) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.6771 (m-80) cc_final: 0.6065 (m-80) REVERT: A 67 GLU cc_start: 0.8291 (tp30) cc_final: 0.7700 (tm-30) REVERT: A 76 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7867 (mp0) REVERT: A 259 LEU cc_start: 0.7793 (tp) cc_final: 0.7305 (tt) REVERT: B 75 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8095 (mtt) REVERT: B 100 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 130 ASP cc_start: 0.8540 (t0) cc_final: 0.8260 (t0) REVERT: B 192 MET cc_start: 0.9185 (tmm) cc_final: 0.8777 (tmm) REVERT: B 250 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7948 (tmm-80) REVERT: C 194 MET cc_start: 0.9203 (ttm) cc_final: 0.8927 (mtt) REVERT: C 233 PHE cc_start: 0.8467 (t80) cc_final: 0.8154 (t80) REVERT: C 251 ASP cc_start: 0.8831 (m-30) cc_final: 0.8566 (m-30) REVERT: a 308 GLU cc_start: 0.8342 (mp0) cc_final: 0.7926 (mt-10) REVERT: a 366 TYR cc_start: 0.8618 (m-80) cc_final: 0.8274 (m-10) REVERT: a 396 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7362 (tm-30) REVERT: a 406 GLN cc_start: 0.9450 (tp40) cc_final: 0.9210 (tp40) REVERT: a 410 MET cc_start: 0.7546 (mtp) cc_final: 0.7310 (mtp) REVERT: b 283 TRP cc_start: 0.7540 (m100) cc_final: 0.7243 (m100) REVERT: b 287 GLU cc_start: 0.9271 (pt0) cc_final: 0.8946 (pp20) REVERT: b 289 GLU cc_start: 0.7832 (mp0) cc_final: 0.7353 (mp0) REVERT: b 303 GLU cc_start: 0.8548 (mp0) cc_final: 0.8171 (mp0) REVERT: b 311 ASP cc_start: 0.9149 (m-30) cc_final: 0.8689 (t0) REVERT: b 401 ASP cc_start: 0.9201 (t70) cc_final: 0.8879 (t0) REVERT: c 304 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8623 (mtmm) REVERT: c 308 GLU cc_start: 0.8279 (mp0) cc_final: 0.7577 (mt-10) REVERT: c 405 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8499 (tm-30) REVERT: c 406 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8244 (tp-100) REVERT: c 410 MET cc_start: 0.7253 (mmt) cc_final: 0.6432 (mmm) outliers start: 28 outliers final: 24 residues processed: 201 average time/residue: 0.2205 time to fit residues: 63.2392 Evaluate side-chains 199 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 312 MET Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 117 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.103839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.080443 restraints weight = 27903.133| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.00 r_work: 0.3232 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 10912 Z= 0.258 Angle : 0.982 20.655 14959 Z= 0.460 Chirality : 0.051 0.524 1903 Planarity : 0.004 0.046 1762 Dihedral : 7.635 55.845 2987 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.73 % Allowed : 17.98 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1038 helix: 0.77 (0.28), residues: 363 sheet: 1.26 (0.46), residues: 127 loop : -0.31 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 210 HIS 0.009 0.001 HIS A 93 PHE 0.012 0.002 PHE c 399 TYR 0.023 0.002 TYR c 366 ARG 0.004 0.001 ARG B 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 33) link_NAG-ASN : angle 2.60127 ( 99) link_ALPHA1-6 : bond 0.01103 ( 3) link_ALPHA1-6 : angle 1.20352 ( 9) link_BETA1-4 : bond 0.00987 ( 36) link_BETA1-4 : angle 2.68248 ( 108) link_ALPHA1-2 : bond 0.00385 ( 3) link_ALPHA1-2 : angle 2.24331 ( 9) link_ALPHA1-3 : bond 0.01219 ( 3) link_ALPHA1-3 : angle 1.32445 ( 9) hydrogen bonds : bond 0.04747 ( 425) hydrogen bonds : angle 5.15130 ( 1065) link_BETA1-6 : bond 0.00231 ( 1) link_BETA1-6 : angle 2.31519 ( 3) SS BOND : bond 0.01156 ( 20) SS BOND : angle 4.66375 ( 40) link_BETA1-3 : bond 0.01308 ( 1) link_BETA1-3 : angle 2.80208 ( 3) covalent geometry : bond 0.00587 (10812) covalent geometry : angle 0.90436 (14679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5685.94 seconds wall clock time: 102 minutes 55.54 seconds (6175.54 seconds total)