Starting phenix.real_space_refine on Fri Feb 14 08:47:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejd_28178/02_2025/8ejd_28178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejd_28178/02_2025/8ejd_28178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejd_28178/02_2025/8ejd_28178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejd_28178/02_2025/8ejd_28178.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejd_28178/02_2025/8ejd_28178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejd_28178/02_2025/8ejd_28178.cif" } resolution = 3.8 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= 0.022 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 6093 2.51 5 N 1524 2.21 5 O 2094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9804 Number of models: 1 Model: "" Number of chains: 36 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1551 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "c" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1551 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "a" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1551 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "b" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "D" 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: "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: 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" 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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: 6.24, per 1000 atoms: 0.64 Number of scatterers: 9804 At special positions: 0 Unit cell: (100.05, 98.9, 102.35, 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 2094 8.00 N 1524 7.00 C 6093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.02 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 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=2.02 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 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=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.02 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA f 3 " - " MAN f 5 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 3 " " NAG Y 1 " - " FUC Y 3 " NAG-ASN " NAG D 1 " - " ASN C 79 " " NAG E 1 " - " ASN C 89 " " NAG F 1 " - " ASN C 99 " " NAG G 1 " - " ASN C 109 " " NAG H 1 " - " ASN C 119 " " NAG I 1 " - " ASN C 167 " " NAG J 1 " - " ASN C 224 " " NAG K 1 " - " ASN c 365 " " NAG L 1 " - " ASN c 373 " " NAG M 1 " - " ASN A 79 " " NAG N 1 " - " ASN A 89 " " NAG O 1 " - " ASN A 99 " " NAG P 1 " - " ASN A 109 " " NAG Q 1 " - " ASN A 119 " " NAG R 1 " - " ASN A 167 " " NAG S 1 " - " ASN A 224 " " NAG T 1 " - " ASN a 365 " " NAG U 1 " - " ASN a 373 " " NAG V 1 " - " ASN B 79 " " NAG W 1 " - " ASN B 89 " " NAG X 1 " - " ASN B 99 " " NAG Y 1 " - " ASN B 109 " " NAG Z 1 " - " ASN B 119 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " " NAG d 1 " - " ASN B 167 " " NAG e 1 " - " ASN B 224 " " NAG f 1 " - " ASN b 365 " " NAG g 1 " - " ASN b 373 " Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 935.5 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 44.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.618A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN C 79 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 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 169 through 172 Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 205 through 213 removed outlier: 4.876A pdb=" N TRP C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 213 " --> pdb=" O TRP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 295 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 308 through 325 removed outlier: 3.814A pdb=" N MET c 312 " --> pdb=" O GLU c 308 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 345 removed outlier: 4.067A pdb=" N LYS c 339 " --> pdb=" O GLN c 335 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 424 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.619A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 79 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 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 169 through 172 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 213 removed outlier: 4.876A pdb=" N TRP A 210 " --> pdb=" O CYS A 207 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 213 " --> pdb=" O TRP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 295 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 308 through 325 removed outlier: 3.814A pdb=" N MET a 312 " --> pdb=" O GLU a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 345 removed outlier: 4.067A pdb=" N LYS a 339 " --> pdb=" O GLN a 335 " (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 424 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.619A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B 79 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 130 through 143 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 169 through 172 Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 205 through 213 removed outlier: 4.876A pdb=" N TRP B 210 " --> pdb=" O CYS B 207 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 213 " --> pdb=" O TRP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 295 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 308 through 325 removed outlier: 3.814A pdb=" N MET b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 345 removed outlier: 4.067A pdb=" N LYS b 339 " --> pdb=" O GLN b 335 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 424 Processing sheet with id=AA1, first strand: chain 'C' and resid 61 through 62 removed outlier: 9.425A pdb=" N TYR c 366 " --> pdb=" O VAL c 388 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N VAL c 388 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS c 368 " --> pdb=" O TRP c 386 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER c 392 " --> pdb=" O SER c 389 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.511A pdb=" N TYR C 219 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 277 through 280 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 62 removed outlier: 9.424A pdb=" N TYR a 366 " --> pdb=" O VAL a 388 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N VAL a 388 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS a 368 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER a 392 " --> pdb=" O SER a 389 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.511A pdb=" N TYR A 219 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 277 through 280 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 62 removed outlier: 9.425A pdb=" N TYR b 366 " --> pdb=" O VAL b 388 " (cutoff:3.500A) removed outlier: 10.869A pdb=" N VAL b 388 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS b 368 " --> pdb=" O TRP b 386 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER b 392 " --> pdb=" O SER b 389 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.511A pdb=" N TYR B 219 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 277 through 280 402 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 3.84 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: 2298 1.33 - 1.46: 3219 1.46 - 1.60: 4329 1.60 - 1.74: 6 1.74 - 1.88: 144 Bond restraints: 9996 Sorted by residual: bond pdb=" CB HIS C 93 " pdb=" CG HIS C 93 " ideal model delta sigma weight residual 1.497 1.419 0.078 1.40e-02 5.10e+03 3.07e+01 bond pdb=" CB HIS A 93 " pdb=" CG HIS A 93 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.04e+01 bond pdb=" CB HIS B 93 " pdb=" CG HIS B 93 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.02e+01 bond pdb=" CB HIS a 374 " pdb=" CG HIS a 374 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" CB HIS c 374 " pdb=" CG HIS c 374 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.40e+01 ... (remaining 9991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 12460 3.16 - 6.33: 995 6.33 - 9.49: 60 9.49 - 12.66: 12 12.66 - 15.82: 9 Bond angle restraints: 13536 Sorted by residual: angle pdb=" N GLY A 198 " pdb=" CA GLY A 198 " pdb=" C GLY A 198 " ideal model delta sigma weight residual 115.42 128.53 -13.11 1.27e+00 6.20e-01 1.07e+02 angle pdb=" N GLY C 198 " pdb=" CA GLY C 198 " pdb=" C GLY C 198 " ideal model delta sigma weight residual 115.42 128.49 -13.07 1.27e+00 6.20e-01 1.06e+02 angle pdb=" N GLY B 198 " pdb=" CA GLY B 198 " pdb=" C GLY B 198 " ideal model delta sigma weight residual 115.42 128.49 -13.07 1.27e+00 6.20e-01 1.06e+02 angle pdb=" N ILE b 345 " pdb=" CA ILE b 345 " pdb=" C ILE b 345 " ideal model delta sigma weight residual 108.58 119.35 -10.77 1.44e+00 4.82e-01 5.60e+01 angle pdb=" N ILE c 345 " pdb=" CA ILE c 345 " pdb=" C ILE c 345 " ideal model delta sigma weight residual 108.58 119.34 -10.76 1.44e+00 4.82e-01 5.59e+01 ... (remaining 13531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 6696 21.47 - 42.94: 195 42.94 - 64.41: 57 64.41 - 85.88: 84 85.88 - 107.35: 48 Dihedral angle restraints: 7080 sinusoidal: 3903 harmonic: 3177 Sorted by residual: dihedral pdb=" CB CYS A 207 " pdb=" SG CYS A 207 " pdb=" SG CYS a 360 " pdb=" CB CYS a 360 " ideal model delta sinusoidal sigma weight residual -86.00 -163.11 77.11 1 1.00e+01 1.00e-02 7.46e+01 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 -163.10 77.10 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS b 360 " pdb=" CB CYS b 360 " ideal model delta sinusoidal sigma weight residual -86.00 -163.09 77.09 1 1.00e+01 1.00e-02 7.46e+01 ... (remaining 7077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 1608 0.309 - 0.618: 132 0.618 - 0.927: 0 0.927 - 1.236: 0 1.236 - 1.545: 3 Chirality restraints: 1743 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.25e+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 -2.70 0.30 2.00e-02 2.50e+03 2.24e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.24e+02 ... (remaining 1740 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 701 " 0.314 2.00e-02 2.50e+03 2.68e-01 8.95e+02 pdb=" C7 NAG c 701 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG c 701 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG c 701 " -0.466 2.00e-02 2.50e+03 pdb=" O7 NAG c 701 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 701 " -0.314 2.00e-02 2.50e+03 2.67e-01 8.94e+02 pdb=" C7 NAG a 701 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG a 701 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG a 701 " 0.466 2.00e-02 2.50e+03 pdb=" O7 NAG a 701 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 701 " 0.314 2.00e-02 2.50e+03 2.67e-01 8.93e+02 pdb=" C7 NAG b 701 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG b 701 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG b 701 " -0.466 2.00e-02 2.50e+03 pdb=" O7 NAG b 701 " 0.052 2.00e-02 2.50e+03 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4092 2.90 - 3.40: 9482 3.40 - 3.90: 16636 3.90 - 4.40: 19107 4.40 - 4.90: 29701 Nonbonded interactions: 79018 Sorted by model distance: nonbonded pdb=" C4 NAG K 1 " pdb=" O6 NAG K 1 " model vdw 2.400 2.776 nonbonded pdb=" C4 NAG f 1 " pdb=" O6 NAG f 1 " model vdw 2.400 2.776 nonbonded pdb=" C4 NAG T 1 " pdb=" O6 NAG T 1 " model vdw 2.400 2.776 nonbonded pdb=" OD2 ASP c 401 " pdb=" NZ LYS a 272 " model vdw 2.409 3.120 nonbonded pdb=" OD2 ASP a 401 " pdb=" NZ LYS b 272 " model vdw 2.409 3.120 ... (remaining 79013 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' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'T' selection = chain 'U' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.070 Find NCS groups from input model: 0.410 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 0.111 9996 Z= 1.358 Angle : 1.832 15.821 13536 Z= 1.132 Chirality : 0.169 1.545 1743 Planarity : 0.019 0.268 1593 Dihedral : 17.205 107.346 4977 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -0.17 (0.24), residues: 1074 helix: -0.57 (0.24), residues: 369 sheet: 1.12 (0.43), residues: 129 loop : 0.06 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.008 TRP A 227 HIS 0.010 0.003 HIS A 115 PHE 0.024 0.005 PHE B 233 TYR 0.063 0.008 TYR b 363 ARG 0.004 0.001 ARG a 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.7515 (m-80) cc_final: 0.7290 (m-80) REVERT: C 130 ASP cc_start: 0.8657 (t0) cc_final: 0.8382 (t0) REVERT: C 189 GLN cc_start: 0.8861 (mt0) cc_final: 0.8450 (mt0) REVERT: c 348 GLN cc_start: 0.8847 (mp10) cc_final: 0.8031 (mp10) REVERT: c 357 ASP cc_start: 0.8930 (t0) cc_final: 0.8690 (t0) REVERT: A 130 ASP cc_start: 0.8492 (t0) cc_final: 0.8284 (t0) REVERT: A 189 GLN cc_start: 0.8888 (mt0) cc_final: 0.8524 (mt0) REVERT: A 194 MET cc_start: 0.8775 (tpp) cc_final: 0.8466 (tpp) REVERT: a 321 GLN cc_start: 0.9343 (mm-40) cc_final: 0.9071 (mm-40) REVERT: a 348 GLN cc_start: 0.8765 (mp10) cc_final: 0.7968 (mp10) REVERT: a 405 GLN cc_start: 0.9028 (tp40) cc_final: 0.8796 (tp-100) REVERT: B 130 ASP cc_start: 0.8695 (t0) cc_final: 0.8336 (t70) REVERT: B 189 GLN cc_start: 0.9038 (mt0) cc_final: 0.8684 (mt0) REVERT: B 244 LEU cc_start: 0.9198 (mt) cc_final: 0.8830 (mt) REVERT: b 357 ASP cc_start: 0.8864 (t0) cc_final: 0.8581 (t0) REVERT: b 405 GLN cc_start: 0.8976 (tp40) cc_final: 0.8616 (tp-100) REVERT: b 409 ASN cc_start: 0.8998 (m-40) cc_final: 0.8636 (m110) REVERT: b 418 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8897 (tt0) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2939 time to fit residues: 136.7972 Evaluate side-chains 200 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS A 170 HIS ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 324 GLN ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.097544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.076691 restraints weight = 25631.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.079686 restraints weight = 14187.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081775 restraints weight = 9941.921| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9996 Z= 0.284 Angle : 0.939 12.252 13536 Z= 0.471 Chirality : 0.057 0.445 1743 Planarity : 0.005 0.049 1593 Dihedral : 14.293 77.554 2934 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.90 % Allowed : 9.94 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.02 (0.25), residues: 1074 helix: 0.21 (0.25), residues: 390 sheet: 0.98 (0.44), residues: 126 loop : -0.26 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP c 386 HIS 0.006 0.001 HIS A 170 PHE 0.013 0.002 PHE B 233 TYR 0.024 0.002 TYR A 62 ARG 0.005 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.6970 (m-80) cc_final: 0.6397 (m-80) REVERT: C 80 MET cc_start: 0.9213 (mmt) cc_final: 0.8810 (tpp) REVERT: C 116 LYS cc_start: 0.8613 (mmtt) cc_final: 0.7776 (mmmt) REVERT: C 130 ASP cc_start: 0.8386 (t0) cc_final: 0.7909 (t0) REVERT: C 189 GLN cc_start: 0.8709 (mt0) cc_final: 0.8449 (mt0) REVERT: C 194 MET cc_start: 0.9075 (tpt) cc_final: 0.8787 (tpt) REVERT: C 210 TRP cc_start: 0.7516 (t-100) cc_final: 0.7295 (t-100) REVERT: c 321 GLN cc_start: 0.9229 (mm110) cc_final: 0.8828 (mm-40) REVERT: c 332 MET cc_start: 0.7890 (tpp) cc_final: 0.7672 (mmm) REVERT: c 351 MET cc_start: 0.9186 (mmm) cc_final: 0.8917 (mmm) REVERT: c 409 ASN cc_start: 0.9359 (m-40) cc_final: 0.8932 (m-40) REVERT: c 410 MET cc_start: 0.7704 (ttm) cc_final: 0.7150 (ttm) REVERT: c 413 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8145 (tm-30) REVERT: c 417 LYS cc_start: 0.8630 (ptmm) cc_final: 0.8230 (pttp) REVERT: A 66 TYR cc_start: 0.6794 (m-80) cc_final: 0.6442 (m-10) REVERT: A 116 LYS cc_start: 0.8493 (mmtm) cc_final: 0.7661 (mmmt) REVERT: A 130 ASP cc_start: 0.7998 (t0) cc_final: 0.7735 (t0) REVERT: A 153 MET cc_start: 0.8279 (tmm) cc_final: 0.7622 (tmm) REVERT: A 194 MET cc_start: 0.9177 (tpp) cc_final: 0.8836 (tpt) REVERT: A 210 TRP cc_start: 0.7678 (t-100) cc_final: 0.7288 (t-100) REVERT: A 227 TRP cc_start: 0.8491 (t60) cc_final: 0.8115 (t60) REVERT: A 235 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7933 (ttm-80) REVERT: a 321 GLN cc_start: 0.9296 (mm-40) cc_final: 0.8727 (mm-40) REVERT: a 324 GLN cc_start: 0.8274 (tm130) cc_final: 0.7932 (tm-30) REVERT: a 401 ASP cc_start: 0.7966 (p0) cc_final: 0.7748 (p0) REVERT: a 405 GLN cc_start: 0.9482 (tp40) cc_final: 0.9038 (tp-100) REVERT: a 409 ASN cc_start: 0.9193 (m-40) cc_final: 0.8877 (m-40) REVERT: a 410 MET cc_start: 0.7937 (ttm) cc_final: 0.7029 (ttm) REVERT: a 413 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 66 TYR cc_start: 0.6672 (m-80) cc_final: 0.5796 (m-10) REVERT: B 116 LYS cc_start: 0.8495 (mmtt) cc_final: 0.7742 (mmmt) REVERT: B 130 ASP cc_start: 0.8234 (t0) cc_final: 0.7755 (t0) REVERT: B 134 MET cc_start: 0.8677 (tpt) cc_final: 0.8462 (tpt) REVERT: B 189 GLN cc_start: 0.8763 (mt0) cc_final: 0.8434 (mt0) REVERT: B 194 MET cc_start: 0.9063 (tpt) cc_final: 0.8860 (tpt) REVERT: B 210 TRP cc_start: 0.7820 (t-100) cc_final: 0.7308 (t-100) REVERT: B 235 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.8008 (ttm-80) REVERT: b 332 MET cc_start: 0.7803 (tpp) cc_final: 0.7579 (tpt) REVERT: b 374 HIS cc_start: 0.8307 (t-90) cc_final: 0.7855 (t-90) REVERT: b 405 GLN cc_start: 0.9475 (tp40) cc_final: 0.9242 (tp-100) REVERT: b 410 MET cc_start: 0.7772 (ttm) cc_final: 0.6753 (ttt) REVERT: b 413 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7375 (tm-30) REVERT: b 417 LYS cc_start: 0.8589 (ptmm) cc_final: 0.8035 (pttt) outliers start: 28 outliers final: 15 residues processed: 264 average time/residue: 0.2514 time to fit residues: 89.0591 Evaluate side-chains 212 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 421 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.092540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071462 restraints weight = 26502.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.074184 restraints weight = 15374.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.076051 restraints weight = 11022.370| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9996 Z= 0.393 Angle : 0.943 13.211 13536 Z= 0.465 Chirality : 0.056 0.419 1743 Planarity : 0.004 0.037 1593 Dihedral : 11.348 57.405 2934 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.42 % Favored : 93.30 % Rotamer: Outliers : 2.80 % Allowed : 12.73 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.06 (0.26), residues: 1074 helix: 0.67 (0.27), residues: 390 sheet: 0.73 (0.45), residues: 126 loop : -0.52 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 386 HIS 0.007 0.002 HIS C 93 PHE 0.016 0.002 PHE A 157 TYR 0.019 0.002 TYR b 371 ARG 0.006 0.001 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.7112 (m-80) cc_final: 0.6886 (m-80) REVERT: C 80 MET cc_start: 0.9171 (mmt) cc_final: 0.8713 (tpp) REVERT: C 116 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8174 (mmmt) REVERT: C 130 ASP cc_start: 0.8274 (t0) cc_final: 0.7815 (t0) REVERT: C 153 MET cc_start: 0.8473 (tmm) cc_final: 0.8172 (tmm) REVERT: C 194 MET cc_start: 0.9105 (tpt) cc_final: 0.8731 (tpt) REVERT: c 409 ASN cc_start: 0.9391 (m-40) cc_final: 0.8841 (m-40) REVERT: c 413 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8255 (tm-30) REVERT: c 418 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8936 (mt-10) REVERT: A 130 ASP cc_start: 0.8059 (t0) cc_final: 0.7778 (t70) REVERT: A 153 MET cc_start: 0.8516 (tmm) cc_final: 0.8139 (tmm) REVERT: A 189 GLN cc_start: 0.8786 (mt0) cc_final: 0.8446 (mm-40) REVERT: A 194 MET cc_start: 0.9305 (tpp) cc_final: 0.8844 (tpt) REVERT: A 235 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.7655 (ttm-80) REVERT: a 321 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9130 (mm110) REVERT: a 324 GLN cc_start: 0.8343 (tm130) cc_final: 0.7751 (tm-30) REVERT: a 351 MET cc_start: 0.9196 (tpp) cc_final: 0.8986 (tpp) REVERT: a 374 HIS cc_start: 0.8479 (t-90) cc_final: 0.8125 (t-90) REVERT: a 405 GLN cc_start: 0.9575 (tp40) cc_final: 0.9185 (tp-100) REVERT: a 410 MET cc_start: 0.8117 (ttm) cc_final: 0.7875 (ttm) REVERT: a 413 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8264 (tm-30) REVERT: B 62 TYR cc_start: 0.7029 (m-80) cc_final: 0.6592 (m-80) REVERT: B 116 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7465 (mmmt) REVERT: B 130 ASP cc_start: 0.8386 (t0) cc_final: 0.7896 (t0) REVERT: B 134 MET cc_start: 0.8821 (tpt) cc_final: 0.8398 (tmm) REVERT: B 189 GLN cc_start: 0.8774 (mt0) cc_final: 0.8535 (mt0) REVERT: B 210 TRP cc_start: 0.7717 (t-100) cc_final: 0.7162 (t-100) REVERT: b 303 GLU cc_start: 0.7976 (tp30) cc_final: 0.7634 (tp30) REVERT: b 357 ASP cc_start: 0.9180 (t0) cc_final: 0.8936 (t70) REVERT: b 374 HIS cc_start: 0.8515 (t-90) cc_final: 0.8280 (t-90) REVERT: b 405 GLN cc_start: 0.9552 (tp40) cc_final: 0.9345 (tp-100) REVERT: b 410 MET cc_start: 0.8006 (ttm) cc_final: 0.7580 (ttm) REVERT: b 413 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7825 (tm-30) REVERT: b 414 MET cc_start: 0.8199 (tmm) cc_final: 0.7700 (ttm) REVERT: b 418 GLU cc_start: 0.9207 (tt0) cc_final: 0.8731 (mt-10) outliers start: 27 outliers final: 17 residues processed: 223 average time/residue: 0.2309 time to fit residues: 71.1525 Evaluate side-chains 203 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 HIS C 209 ASN ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN a 416 GLN B 115 HIS B 209 ASN b 324 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.093747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072702 restraints weight = 26524.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.075489 restraints weight = 15177.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.077412 restraints weight = 10887.141| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9996 Z= 0.235 Angle : 0.805 10.262 13536 Z= 0.395 Chirality : 0.051 0.419 1743 Planarity : 0.003 0.045 1593 Dihedral : 9.574 52.736 2934 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.59 % Allowed : 14.18 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.08 (0.26), residues: 1074 helix: 0.59 (0.27), residues: 408 sheet: 0.54 (0.45), residues: 126 loop : -0.64 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 386 HIS 0.005 0.001 HIS C 93 PHE 0.008 0.002 PHE B 157 TYR 0.021 0.002 TYR b 371 ARG 0.006 0.001 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.5444 (m-10) cc_final: 0.4609 (m-10) REVERT: C 116 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8148 (mmmt) REVERT: C 130 ASP cc_start: 0.8390 (t0) cc_final: 0.7869 (t0) REVERT: C 153 MET cc_start: 0.8569 (tmm) cc_final: 0.7925 (tmm) REVERT: C 189 GLN cc_start: 0.8822 (mt0) cc_final: 0.8399 (mm-40) REVERT: C 194 MET cc_start: 0.9068 (tpt) cc_final: 0.8777 (tpt) REVERT: c 410 MET cc_start: 0.7880 (ttm) cc_final: 0.6923 (ttt) REVERT: c 413 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8356 (tm-30) REVERT: c 418 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8897 (mt-10) REVERT: A 66 TYR cc_start: 0.6631 (m-80) cc_final: 0.5760 (m-10) REVERT: A 130 ASP cc_start: 0.8034 (t0) cc_final: 0.7713 (t70) REVERT: A 153 MET cc_start: 0.8635 (tmm) cc_final: 0.8238 (tmm) REVERT: A 189 GLN cc_start: 0.8836 (mt0) cc_final: 0.8468 (mm-40) REVERT: A 194 MET cc_start: 0.9264 (tpp) cc_final: 0.8918 (tpt) REVERT: a 324 GLN cc_start: 0.8357 (tm130) cc_final: 0.8037 (tm-30) REVERT: a 332 MET cc_start: 0.7420 (mmm) cc_final: 0.7203 (tpp) REVERT: a 357 ASP cc_start: 0.9095 (t70) cc_final: 0.8691 (t70) REVERT: a 374 HIS cc_start: 0.8358 (t-90) cc_final: 0.8037 (t-90) REVERT: a 405 GLN cc_start: 0.9571 (tp40) cc_final: 0.9359 (tp-100) REVERT: a 410 MET cc_start: 0.8014 (ttm) cc_final: 0.7171 (ttt) REVERT: a 413 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8272 (tm-30) REVERT: B 62 TYR cc_start: 0.6885 (m-80) cc_final: 0.6570 (m-80) REVERT: B 116 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7460 (mmmt) REVERT: B 122 ASP cc_start: 0.9357 (m-30) cc_final: 0.9145 (m-30) REVERT: B 125 LYS cc_start: 0.9062 (mmtm) cc_final: 0.8832 (mmtm) REVERT: B 130 ASP cc_start: 0.8418 (t0) cc_final: 0.7964 (t0) REVERT: B 189 GLN cc_start: 0.8812 (mt0) cc_final: 0.7969 (mt0) REVERT: B 210 TRP cc_start: 0.7648 (t-100) cc_final: 0.6717 (t-100) REVERT: B 235 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.8100 (ttm-80) REVERT: b 303 GLU cc_start: 0.7945 (tp30) cc_final: 0.7616 (tp30) REVERT: b 357 ASP cc_start: 0.9124 (t0) cc_final: 0.8888 (t70) REVERT: b 374 HIS cc_start: 0.8375 (t-90) cc_final: 0.7915 (t-90) REVERT: b 405 GLN cc_start: 0.9553 (tp40) cc_final: 0.9311 (tp-100) REVERT: b 410 MET cc_start: 0.8017 (ttm) cc_final: 0.7662 (ttm) REVERT: b 413 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7872 (tm-30) REVERT: b 418 GLU cc_start: 0.9222 (tt0) cc_final: 0.8976 (tm-30) REVERT: b 420 MET cc_start: 0.7975 (mmt) cc_final: 0.7758 (mmp) outliers start: 25 outliers final: 12 residues processed: 223 average time/residue: 0.2426 time to fit residues: 73.7745 Evaluate side-chains 200 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN a 416 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.093941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073028 restraints weight = 26953.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075855 restraints weight = 15362.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077833 restraints weight = 10990.940| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9996 Z= 0.215 Angle : 0.786 12.002 13536 Z= 0.386 Chirality : 0.050 0.415 1743 Planarity : 0.004 0.046 1593 Dihedral : 8.933 52.335 2934 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.69 % Allowed : 16.46 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.14 (0.26), residues: 1074 helix: 0.67 (0.27), residues: 408 sheet: 0.79 (0.53), residues: 96 loop : -0.80 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 386 HIS 0.004 0.001 HIS A 93 PHE 0.033 0.002 PHE A 233 TYR 0.019 0.001 TYR C 62 ARG 0.007 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.960 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: C 116 LYS cc_start: 0.8568 (mmtt) cc_final: 0.7700 (mmmt) REVERT: C 130 ASP cc_start: 0.8342 (t0) cc_final: 0.7669 (t70) REVERT: C 153 MET cc_start: 0.8548 (tmm) cc_final: 0.7913 (tmm) REVERT: C 189 GLN cc_start: 0.8837 (mt0) cc_final: 0.8310 (mm-40) REVERT: C 194 MET cc_start: 0.9069 (tpt) cc_final: 0.8839 (tpt) REVERT: c 303 GLU cc_start: 0.7727 (tp30) cc_final: 0.7421 (tp30) REVERT: c 347 ASP cc_start: 0.8837 (p0) cc_final: 0.8334 (t70) REVERT: c 348 GLN cc_start: 0.8790 (mm-40) cc_final: 0.7935 (mm110) REVERT: c 349 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9233 (tp) REVERT: c 410 MET cc_start: 0.7874 (ttm) cc_final: 0.6926 (ttt) REVERT: c 413 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8382 (tm-30) REVERT: c 418 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8915 (mt-10) REVERT: A 66 TYR cc_start: 0.6681 (m-80) cc_final: 0.5868 (m-10) REVERT: A 130 ASP cc_start: 0.8037 (t0) cc_final: 0.7676 (t0) REVERT: A 153 MET cc_start: 0.8593 (tmm) cc_final: 0.8164 (tmm) REVERT: A 189 GLN cc_start: 0.8766 (mt0) cc_final: 0.8256 (mm-40) REVERT: A 194 MET cc_start: 0.9278 (tpp) cc_final: 0.8911 (tpt) REVERT: A 235 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7629 (ttm-80) REVERT: a 357 ASP cc_start: 0.9065 (t70) cc_final: 0.8654 (t70) REVERT: a 374 HIS cc_start: 0.8302 (t-90) cc_final: 0.7901 (t-90) REVERT: a 405 GLN cc_start: 0.9591 (tp40) cc_final: 0.9386 (tp-100) REVERT: a 410 MET cc_start: 0.7978 (ttm) cc_final: 0.6973 (ttt) REVERT: a 413 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8295 (tm-30) REVERT: B 116 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7486 (mmmt) REVERT: B 122 ASP cc_start: 0.9398 (m-30) cc_final: 0.9142 (m-30) REVERT: B 125 LYS cc_start: 0.9090 (mmtm) cc_final: 0.8871 (mmtm) REVERT: B 130 ASP cc_start: 0.8391 (t0) cc_final: 0.7900 (t0) REVERT: B 134 MET cc_start: 0.8562 (mmm) cc_final: 0.8211 (tmm) REVERT: B 189 GLN cc_start: 0.8811 (mt0) cc_final: 0.7701 (mt0) REVERT: B 210 TRP cc_start: 0.7606 (t-100) cc_final: 0.6498 (t-100) REVERT: B 235 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.7996 (ttm-80) REVERT: b 303 GLU cc_start: 0.8017 (tp30) cc_final: 0.7495 (tp30) REVERT: b 357 ASP cc_start: 0.9151 (t0) cc_final: 0.8891 (t70) REVERT: b 374 HIS cc_start: 0.8459 (t-90) cc_final: 0.8056 (t-90) REVERT: b 405 GLN cc_start: 0.9549 (tp40) cc_final: 0.9286 (tp-100) REVERT: b 410 MET cc_start: 0.8035 (ttm) cc_final: 0.7766 (ttm) REVERT: b 414 MET cc_start: 0.8010 (tmm) cc_final: 0.7650 (ttm) REVERT: b 418 GLU cc_start: 0.9218 (tt0) cc_final: 0.8784 (mt-10) outliers start: 26 outliers final: 10 residues processed: 211 average time/residue: 0.2511 time to fit residues: 71.1463 Evaluate side-chains 193 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN c 416 GLN A 90 ASN a 416 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.095155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075320 restraints weight = 27398.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077928 restraints weight = 16673.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079758 restraints weight = 12283.397| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9996 Z= 0.224 Angle : 0.759 11.017 13536 Z= 0.372 Chirality : 0.049 0.413 1743 Planarity : 0.003 0.045 1593 Dihedral : 8.593 52.159 2934 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.38 % Allowed : 16.87 % Favored : 80.75 % 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: 0.00 (0.26), residues: 1074 helix: 1.05 (0.28), residues: 384 sheet: 0.57 (0.53), residues: 96 loop : -0.80 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 386 HIS 0.005 0.001 HIS a 305 PHE 0.024 0.002 PHE A 233 TYR 0.015 0.001 TYR b 371 ARG 0.006 0.001 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7894 (mmmt) REVERT: C 130 ASP cc_start: 0.8494 (t0) cc_final: 0.7957 (t0) REVERT: C 153 MET cc_start: 0.8567 (tmm) cc_final: 0.7974 (tmm) REVERT: C 189 GLN cc_start: 0.8795 (mt0) cc_final: 0.8400 (mm-40) REVERT: c 347 ASP cc_start: 0.8749 (p0) cc_final: 0.8121 (t70) REVERT: c 348 GLN cc_start: 0.8784 (mm-40) cc_final: 0.7987 (mm110) REVERT: c 349 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9270 (tp) REVERT: c 351 MET cc_start: 0.9110 (mmm) cc_final: 0.8758 (mmm) REVERT: c 413 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 130 ASP cc_start: 0.8233 (t0) cc_final: 0.7896 (t70) REVERT: A 153 MET cc_start: 0.8620 (tmm) cc_final: 0.8250 (tmm) REVERT: A 189 GLN cc_start: 0.8717 (mt0) cc_final: 0.8188 (mm-40) REVERT: A 194 MET cc_start: 0.9202 (tpp) cc_final: 0.8936 (tpt) REVERT: A 235 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7684 (ttm-80) REVERT: a 351 MET cc_start: 0.9163 (tpp) cc_final: 0.8882 (mmm) REVERT: a 357 ASP cc_start: 0.8959 (t70) cc_final: 0.8627 (t70) REVERT: a 374 HIS cc_start: 0.8175 (t-90) cc_final: 0.7909 (t-90) REVERT: a 403 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8068 (tp) REVERT: a 410 MET cc_start: 0.8003 (ttm) cc_final: 0.7694 (ttm) REVERT: a 413 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 116 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7145 (mmmt) REVERT: B 122 ASP cc_start: 0.9184 (m-30) cc_final: 0.8951 (m-30) REVERT: B 125 LYS cc_start: 0.9078 (mmtm) cc_final: 0.8848 (mmtm) REVERT: B 130 ASP cc_start: 0.8521 (t0) cc_final: 0.8192 (t0) REVERT: B 189 GLN cc_start: 0.8719 (mt0) cc_final: 0.8437 (mm-40) REVERT: b 374 HIS cc_start: 0.8143 (t-90) cc_final: 0.7781 (t70) REVERT: b 409 ASN cc_start: 0.9362 (m110) cc_final: 0.9110 (m-40) REVERT: b 410 MET cc_start: 0.8194 (ttm) cc_final: 0.7727 (ttm) REVERT: b 413 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7934 (tm-30) REVERT: b 418 GLU cc_start: 0.9144 (tt0) cc_final: 0.8911 (tm-30) outliers start: 23 outliers final: 14 residues processed: 204 average time/residue: 0.2629 time to fit residues: 73.0027 Evaluate side-chains 201 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 416 GLN Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 0.0020 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 185 ASN C 209 ASN A 90 ASN a 416 GLN B 90 ASN b 405 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.096246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077101 restraints weight = 26506.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079665 restraints weight = 15767.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081514 restraints weight = 11443.556| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9996 Z= 0.196 Angle : 0.743 7.683 13536 Z= 0.365 Chirality : 0.047 0.411 1743 Planarity : 0.004 0.108 1593 Dihedral : 8.265 52.040 2934 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.86 % Allowed : 18.12 % 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: -0.19 (0.26), residues: 1074 helix: 0.67 (0.27), residues: 408 sheet: 0.62 (0.53), residues: 96 loop : -0.83 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 386 HIS 0.004 0.001 HIS c 305 PHE 0.022 0.001 PHE A 233 TYR 0.017 0.001 TYR c 278 ARG 0.010 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 1.138 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: C 116 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7492 (mmmt) REVERT: C 130 ASP cc_start: 0.8468 (t0) cc_final: 0.7873 (t0) REVERT: C 153 MET cc_start: 0.8560 (tmm) cc_final: 0.7983 (tmm) REVERT: C 194 MET cc_start: 0.9092 (tpt) cc_final: 0.8788 (tpt) REVERT: C 211 ASP cc_start: 0.8488 (m-30) cc_final: 0.8221 (m-30) REVERT: C 246 SER cc_start: 0.8671 (p) cc_final: 0.7247 (p) REVERT: c 287 GLU cc_start: 0.7735 (tp30) cc_final: 0.7516 (tp30) REVERT: c 347 ASP cc_start: 0.8684 (p0) cc_final: 0.8008 (t70) REVERT: c 348 GLN cc_start: 0.8757 (mm-40) cc_final: 0.7983 (mm110) REVERT: c 349 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9255 (tp) REVERT: c 409 ASN cc_start: 0.9374 (m-40) cc_final: 0.8964 (m-40) REVERT: c 410 MET cc_start: 0.7764 (ttm) cc_final: 0.6880 (ttt) REVERT: c 413 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8293 (tm-30) REVERT: A 116 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8042 (mmtm) REVERT: A 130 ASP cc_start: 0.8193 (t0) cc_final: 0.7854 (t0) REVERT: A 153 MET cc_start: 0.8625 (tmm) cc_final: 0.8257 (tmm) REVERT: A 189 GLN cc_start: 0.8760 (mt0) cc_final: 0.8290 (mm-40) REVERT: A 194 MET cc_start: 0.9206 (tpp) cc_final: 0.8941 (tpt) REVERT: A 235 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7694 (ttm-80) REVERT: a 347 ASP cc_start: 0.8226 (t70) cc_final: 0.7930 (t70) REVERT: a 348 GLN cc_start: 0.8698 (mp10) cc_final: 0.8305 (mt0) REVERT: a 351 MET cc_start: 0.9160 (tpp) cc_final: 0.8839 (mmm) REVERT: a 357 ASP cc_start: 0.8915 (t70) cc_final: 0.8598 (t70) REVERT: a 374 HIS cc_start: 0.8115 (t-90) cc_final: 0.7832 (t-90) REVERT: a 403 ILE cc_start: 0.8479 (pt) cc_final: 0.8187 (tp) REVERT: a 410 MET cc_start: 0.7989 (ttm) cc_final: 0.7632 (ttm) REVERT: a 413 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 90 ASN cc_start: 0.6761 (OUTLIER) cc_final: 0.6487 (t0) REVERT: B 116 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7041 (mmmt) REVERT: B 122 ASP cc_start: 0.9178 (m-30) cc_final: 0.8959 (m-30) REVERT: B 130 ASP cc_start: 0.8565 (t0) cc_final: 0.8289 (t0) REVERT: B 189 GLN cc_start: 0.8752 (mt0) cc_final: 0.8450 (mm-40) REVERT: B 235 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8200 (ttm-80) REVERT: b 357 ASP cc_start: 0.9088 (t0) cc_final: 0.8845 (t70) REVERT: b 374 HIS cc_start: 0.8057 (t-90) cc_final: 0.7785 (t-90) REVERT: b 410 MET cc_start: 0.8136 (ttm) cc_final: 0.7590 (ttm) REVERT: b 413 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7819 (tm-30) REVERT: b 414 MET cc_start: 0.8151 (tmm) cc_final: 0.7633 (ttm) REVERT: b 418 GLU cc_start: 0.9100 (tt0) cc_final: 0.8716 (mt-10) outliers start: 18 outliers final: 12 residues processed: 201 average time/residue: 0.2579 time to fit residues: 69.6233 Evaluate side-chains 199 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 81 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN a 416 GLN B 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.095943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076028 restraints weight = 27416.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078615 restraints weight = 16568.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.080398 restraints weight = 12214.535| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9996 Z= 0.227 Angle : 0.751 7.470 13536 Z= 0.367 Chirality : 0.047 0.406 1743 Planarity : 0.003 0.045 1593 Dihedral : 8.122 52.418 2934 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.38 % Allowed : 18.01 % Favored : 79.61 % 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: -0.04 (0.26), residues: 1074 helix: 1.02 (0.28), residues: 387 sheet: 0.56 (0.54), residues: 96 loop : -0.84 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 386 HIS 0.005 0.001 HIS C 92 PHE 0.019 0.001 PHE A 233 TYR 0.020 0.001 TYR B 62 ARG 0.006 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8068 (mmtt) REVERT: C 130 ASP cc_start: 0.8473 (t0) cc_final: 0.7895 (t0) REVERT: C 153 MET cc_start: 0.8523 (tmm) cc_final: 0.7923 (tmm) REVERT: C 189 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8313 (mp10) REVERT: C 194 MET cc_start: 0.9120 (tpt) cc_final: 0.8813 (tpt) REVERT: C 246 SER cc_start: 0.8628 (p) cc_final: 0.7618 (p) REVERT: c 287 GLU cc_start: 0.7785 (tp30) cc_final: 0.7581 (tp30) REVERT: c 347 ASP cc_start: 0.8639 (p0) cc_final: 0.8180 (t0) REVERT: c 348 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8049 (mm110) REVERT: c 349 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9289 (tp) REVERT: c 409 ASN cc_start: 0.9343 (m-40) cc_final: 0.8949 (m-40) REVERT: c 410 MET cc_start: 0.7819 (ttm) cc_final: 0.6993 (ttm) REVERT: c 413 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 116 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8081 (mmtm) REVERT: A 130 ASP cc_start: 0.8227 (t0) cc_final: 0.7871 (t0) REVERT: A 153 MET cc_start: 0.8626 (tmm) cc_final: 0.8202 (tmm) REVERT: A 189 GLN cc_start: 0.8742 (mt0) cc_final: 0.8255 (mm-40) REVERT: A 194 MET cc_start: 0.9233 (tpp) cc_final: 0.8917 (tpt) REVERT: A 235 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7695 (ttm-80) REVERT: a 278 TYR cc_start: 0.8873 (t80) cc_final: 0.8668 (t80) REVERT: a 303 GLU cc_start: 0.7944 (tp30) cc_final: 0.7695 (tp30) REVERT: a 312 MET cc_start: 0.8442 (mmm) cc_final: 0.8029 (mmp) REVERT: a 347 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7997 (t70) REVERT: a 348 GLN cc_start: 0.8738 (mp10) cc_final: 0.8324 (mt0) REVERT: a 351 MET cc_start: 0.9128 (tpp) cc_final: 0.8773 (mmm) REVERT: a 357 ASP cc_start: 0.8946 (t70) cc_final: 0.8598 (t70) REVERT: a 374 HIS cc_start: 0.8244 (t-90) cc_final: 0.7840 (t-90) REVERT: a 403 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8164 (tp) REVERT: a 410 MET cc_start: 0.8039 (ttm) cc_final: 0.7765 (ttm) REVERT: a 413 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8256 (tm-30) REVERT: B 116 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7233 (mmmt) REVERT: B 122 ASP cc_start: 0.9272 (m-30) cc_final: 0.9043 (m-30) REVERT: B 125 LYS cc_start: 0.9149 (mmtm) cc_final: 0.8921 (mmtm) REVERT: B 130 ASP cc_start: 0.8576 (t0) cc_final: 0.8325 (t0) REVERT: B 189 GLN cc_start: 0.8732 (mt0) cc_final: 0.8416 (mm-40) REVERT: B 214 MET cc_start: 0.8806 (ttm) cc_final: 0.8578 (mtm) REVERT: B 235 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8184 (ttm-80) REVERT: b 357 ASP cc_start: 0.9129 (t0) cc_final: 0.8870 (t70) REVERT: b 374 HIS cc_start: 0.8185 (t-90) cc_final: 0.7815 (t-90) REVERT: b 418 GLU cc_start: 0.9173 (tt0) cc_final: 0.8917 (tm-30) outliers start: 23 outliers final: 12 residues processed: 201 average time/residue: 0.2503 time to fit residues: 67.6934 Evaluate side-chains 193 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 359 MET Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN b 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.096175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.076987 restraints weight = 26493.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.079614 restraints weight = 15779.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.081402 restraints weight = 11434.058| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9996 Z= 0.214 Angle : 0.751 7.447 13536 Z= 0.368 Chirality : 0.047 0.401 1743 Planarity : 0.004 0.044 1593 Dihedral : 7.944 53.120 2934 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.07 % Allowed : 18.53 % Favored : 79.40 % 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: -0.02 (0.26), residues: 1074 helix: 0.98 (0.27), residues: 405 sheet: 0.63 (0.54), residues: 96 loop : -0.85 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 210 HIS 0.005 0.001 HIS c 305 PHE 0.018 0.001 PHE A 233 TYR 0.023 0.001 TYR a 371 ARG 0.007 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 1.098 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: C 116 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7956 (mmtt) REVERT: C 130 ASP cc_start: 0.8510 (t0) cc_final: 0.7971 (t0) REVERT: C 153 MET cc_start: 0.8520 (tmm) cc_final: 0.7948 (tmm) REVERT: C 189 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8448 (mp10) REVERT: C 194 MET cc_start: 0.9044 (tpt) cc_final: 0.8730 (tpt) REVERT: C 246 SER cc_start: 0.8498 (p) cc_final: 0.7520 (p) REVERT: c 347 ASP cc_start: 0.8602 (p0) cc_final: 0.8176 (t70) REVERT: c 348 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8053 (mm110) REVERT: c 413 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 75 MET cc_start: 0.9042 (mmt) cc_final: 0.8625 (mmt) REVERT: A 116 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8013 (mmtm) REVERT: A 130 ASP cc_start: 0.8269 (t0) cc_final: 0.7927 (t70) REVERT: A 153 MET cc_start: 0.8498 (tmm) cc_final: 0.7729 (tmm) REVERT: A 189 GLN cc_start: 0.8732 (mt0) cc_final: 0.8270 (mm-40) REVERT: A 194 MET cc_start: 0.9172 (tpp) cc_final: 0.8894 (tpt) REVERT: A 235 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7683 (ttm-80) REVERT: a 278 TYR cc_start: 0.8885 (t80) cc_final: 0.8659 (t80) REVERT: a 303 GLU cc_start: 0.7838 (tp30) cc_final: 0.7595 (tp30) REVERT: a 347 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8000 (t70) REVERT: a 348 GLN cc_start: 0.8678 (mp10) cc_final: 0.8327 (mt0) REVERT: a 351 MET cc_start: 0.9099 (tpp) cc_final: 0.8757 (mmm) REVERT: a 357 ASP cc_start: 0.8942 (t70) cc_final: 0.8635 (t70) REVERT: a 374 HIS cc_start: 0.8085 (t-90) cc_final: 0.7870 (t-90) REVERT: a 403 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8136 (tp) REVERT: a 410 MET cc_start: 0.8062 (ttm) cc_final: 0.7718 (ttm) REVERT: a 413 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8195 (tm-30) REVERT: a 414 MET cc_start: 0.8083 (tmm) cc_final: 0.7656 (ttm) REVERT: B 116 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7175 (mmmt) REVERT: B 122 ASP cc_start: 0.9189 (m-30) cc_final: 0.8983 (m-30) REVERT: B 125 LYS cc_start: 0.9166 (mmtm) cc_final: 0.8942 (mmtm) REVERT: B 130 ASP cc_start: 0.8621 (t0) cc_final: 0.8421 (t0) REVERT: B 235 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8221 (ttm-80) REVERT: b 311 ASP cc_start: 0.9004 (m-30) cc_final: 0.8475 (t0) REVERT: b 349 LEU cc_start: 0.9244 (tp) cc_final: 0.8928 (tt) REVERT: b 357 ASP cc_start: 0.9137 (t0) cc_final: 0.8921 (t70) REVERT: b 374 HIS cc_start: 0.8113 (t-90) cc_final: 0.7873 (t-90) REVERT: b 413 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7897 (tm-30) REVERT: b 414 MET cc_start: 0.8147 (tmm) cc_final: 0.7612 (ttm) REVERT: b 418 GLU cc_start: 0.9119 (tt0) cc_final: 0.8748 (mt-10) outliers start: 20 outliers final: 14 residues processed: 199 average time/residue: 0.2551 time to fit residues: 68.2305 Evaluate side-chains 194 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain a residue 419 TYR Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 419 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN A 90 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.096038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076984 restraints weight = 26303.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.079583 restraints weight = 15554.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.081390 restraints weight = 11309.446| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9996 Z= 0.218 Angle : 0.774 9.204 13536 Z= 0.379 Chirality : 0.047 0.406 1743 Planarity : 0.004 0.045 1593 Dihedral : 7.828 53.394 2934 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.17 % Allowed : 19.05 % Favored : 78.78 % 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: -0.01 (0.26), residues: 1074 helix: 1.03 (0.27), residues: 405 sheet: 0.63 (0.55), residues: 96 loop : -0.88 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 210 HIS 0.006 0.001 HIS c 305 PHE 0.017 0.001 PHE A 233 TYR 0.030 0.001 TYR B 66 ARG 0.006 0.000 ARG C 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 1.034 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: C 116 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7922 (mmtt) REVERT: C 130 ASP cc_start: 0.8539 (t0) cc_final: 0.8025 (t0) REVERT: C 153 MET cc_start: 0.8521 (tmm) cc_final: 0.7948 (tmm) REVERT: C 194 MET cc_start: 0.9037 (tpt) cc_final: 0.8727 (tpt) REVERT: C 246 SER cc_start: 0.8450 (p) cc_final: 0.7627 (p) REVERT: c 332 MET cc_start: 0.7681 (tpp) cc_final: 0.7450 (tpp) REVERT: c 347 ASP cc_start: 0.8527 (p0) cc_final: 0.8232 (t70) REVERT: c 348 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8086 (mm110) REVERT: c 410 MET cc_start: 0.7876 (ttm) cc_final: 0.7157 (ttm) REVERT: c 413 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 75 MET cc_start: 0.9021 (mmt) cc_final: 0.8644 (mmt) REVERT: A 116 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8011 (mmtm) REVERT: A 130 ASP cc_start: 0.8294 (t0) cc_final: 0.7941 (t70) REVERT: A 153 MET cc_start: 0.8491 (tmm) cc_final: 0.7726 (tmm) REVERT: A 194 MET cc_start: 0.9157 (tpp) cc_final: 0.8892 (tpt) REVERT: A 235 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7693 (ttm-80) REVERT: a 278 TYR cc_start: 0.8854 (t80) cc_final: 0.8607 (t80) REVERT: a 303 GLU cc_start: 0.7752 (tp30) cc_final: 0.7534 (tp30) REVERT: a 347 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8048 (t70) REVERT: a 348 GLN cc_start: 0.8663 (mp10) cc_final: 0.8384 (mt0) REVERT: a 351 MET cc_start: 0.9119 (tpp) cc_final: 0.8784 (mmm) REVERT: a 357 ASP cc_start: 0.8945 (t70) cc_final: 0.8652 (t70) REVERT: a 374 HIS cc_start: 0.8123 (t-90) cc_final: 0.7905 (t-90) REVERT: a 403 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8157 (tp) REVERT: a 410 MET cc_start: 0.8018 (ttm) cc_final: 0.7510 (ttm) REVERT: a 413 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8251 (tm-30) REVERT: a 414 MET cc_start: 0.8131 (tmm) cc_final: 0.7219 (ttt) REVERT: B 116 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7236 (mtpt) REVERT: B 130 ASP cc_start: 0.8636 (t0) cc_final: 0.8436 (t0) REVERT: b 311 ASP cc_start: 0.8997 (m-30) cc_final: 0.8630 (t0) REVERT: b 357 ASP cc_start: 0.9155 (t0) cc_final: 0.8863 (t70) REVERT: b 374 HIS cc_start: 0.8134 (t-90) cc_final: 0.7785 (t-90) REVERT: b 410 MET cc_start: 0.8172 (ttm) cc_final: 0.7451 (ttm) REVERT: b 414 MET cc_start: 0.8173 (tmm) cc_final: 0.7919 (ttm) REVERT: b 418 GLU cc_start: 0.9120 (tt0) cc_final: 0.8751 (mt-10) outliers start: 21 outliers final: 15 residues processed: 199 average time/residue: 0.2492 time to fit residues: 66.9761 Evaluate side-chains 197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 419 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 405 GLN A 90 ASN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN b 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.096778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.077573 restraints weight = 26247.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.080137 restraints weight = 15713.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.081937 restraints weight = 11448.990| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 9996 Z= 0.283 Angle : 1.024 59.200 13536 Z= 0.557 Chirality : 0.047 0.406 1743 Planarity : 0.004 0.045 1593 Dihedral : 7.849 53.407 2934 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.01 % Favored : 91.90 % Rotamer: Outliers : 2.28 % Allowed : 20.08 % Favored : 77.64 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.01 (0.26), residues: 1074 helix: 1.04 (0.27), residues: 405 sheet: 0.63 (0.55), residues: 96 loop : -0.90 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 210 HIS 0.005 0.001 HIS c 305 PHE 0.016 0.001 PHE A 233 TYR 0.026 0.001 TYR B 66 ARG 0.068 0.001 ARG A 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2905.20 seconds wall clock time: 53 minutes 28.61 seconds (3208.61 seconds total)