Starting phenix.real_space_refine on Sun Dec 29 06:29:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejd_28178/12_2024/8ejd_28178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejd_28178/12_2024/8ejd_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_28178/12_2024/8ejd_28178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejd_28178/12_2024/8ejd_28178.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejd_28178/12_2024/8ejd_28178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejd_28178/12_2024/8ejd_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.43, per 1000 atoms: 0.66 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: 3.84 Conformation dependent library (CDL) restraints added in 972.9 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: 1.02 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: 2.77 Time building geometry restraints manager: 4.23 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: 0.780 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.820 Find NCS groups from input model: 0.440 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.590 ------------------------------------------------------------------------------- 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 : 1.089 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: 0.2892 time to fit residues: 135.5192 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 : 1.109 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 1.190 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: 0.7299 (m-80) cc_final: 0.7053 (m-80) REVERT: C 116 LYS cc_start: 0.8358 (mmtt) cc_final: 0.7644 (mmmt) REVERT: C 130 ASP cc_start: 0.8699 (t0) cc_final: 0.8311 (t0) REVERT: C 194 MET cc_start: 0.8863 (tpt) cc_final: 0.8648 (tpt) REVERT: c 321 GLN cc_start: 0.9466 (mm110) cc_final: 0.9093 (mm-40) REVERT: c 332 MET cc_start: 0.7875 (tpp) cc_final: 0.7277 (mmm) REVERT: c 351 MET cc_start: 0.9089 (mmm) cc_final: 0.8860 (mmm) REVERT: c 409 ASN cc_start: 0.9167 (m-40) cc_final: 0.8838 (m-40) REVERT: c 410 MET cc_start: 0.7633 (ttm) cc_final: 0.7085 (ttm) REVERT: c 413 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7518 (tm-30) REVERT: c 417 LYS cc_start: 0.8763 (ptmm) cc_final: 0.8363 (pttp) REVERT: A 66 TYR cc_start: 0.7321 (m-80) cc_final: 0.7071 (m-10) REVERT: A 116 LYS cc_start: 0.8356 (mmtm) cc_final: 0.7618 (mmmt) REVERT: A 153 MET cc_start: 0.8377 (tmm) cc_final: 0.7925 (tmm) REVERT: A 210 TRP cc_start: 0.7634 (t-100) cc_final: 0.7368 (t-100) REVERT: A 227 TRP cc_start: 0.8610 (t60) cc_final: 0.8342 (t60) REVERT: a 321 GLN cc_start: 0.9338 (mm-40) cc_final: 0.9028 (mm-40) REVERT: a 324 GLN cc_start: 0.8468 (tm130) cc_final: 0.8215 (tm-30) REVERT: a 405 GLN cc_start: 0.9140 (tp40) cc_final: 0.8843 (tp-100) REVERT: a 409 ASN cc_start: 0.9036 (m-40) cc_final: 0.8706 (m-40) REVERT: a 410 MET cc_start: 0.7740 (ttm) cc_final: 0.6955 (ttm) REVERT: a 413 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7427 (tm-30) REVERT: B 66 TYR cc_start: 0.7253 (m-80) cc_final: 0.6572 (m-10) REVERT: B 116 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7472 (mmmt) REVERT: B 130 ASP cc_start: 0.8498 (t0) cc_final: 0.8164 (t0) REVERT: B 194 MET cc_start: 0.8867 (tpt) cc_final: 0.8646 (tpt) REVERT: B 210 TRP cc_start: 0.7763 (t-100) cc_final: 0.7368 (t-100) REVERT: b 332 MET cc_start: 0.7799 (tpp) cc_final: 0.7594 (tpt) REVERT: b 410 MET cc_start: 0.7722 (ttm) cc_final: 0.6816 (ttt) REVERT: b 413 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6922 (tm-30) REVERT: b 417 LYS cc_start: 0.8748 (ptmm) cc_final: 0.8229 (pttt) outliers start: 28 outliers final: 15 residues processed: 264 average time/residue: 0.2425 time to fit residues: 86.1558 Evaluate side-chains 211 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9996 Z= 0.247 Angle : 0.863 12.233 13536 Z= 0.427 Chirality : 0.053 0.385 1743 Planarity : 0.004 0.041 1593 Dihedral : 11.154 55.725 2934 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.77 % Favored : 93.95 % Rotamer: Outliers : 2.28 % Allowed : 12.42 % Favored : 85.30 % 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: 0.04 (0.26), residues: 1074 helix: 0.42 (0.26), residues: 408 sheet: 0.73 (0.45), residues: 126 loop : -0.36 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 386 HIS 0.005 0.001 HIS b 305 PHE 0.013 0.002 PHE A 157 TYR 0.023 0.002 TYR b 371 ARG 0.005 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 247 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 1.051 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: C 66 TYR cc_start: 0.6875 (m-10) cc_final: 0.6250 (m-10) REVERT: C 116 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7672 (mmmt) REVERT: C 130 ASP cc_start: 0.8373 (t0) cc_final: 0.7999 (t0) REVERT: C 153 MET cc_start: 0.8651 (tmm) cc_final: 0.8212 (tmm) REVERT: C 194 MET cc_start: 0.8950 (tpt) cc_final: 0.8701 (tpt) REVERT: c 332 MET cc_start: 0.7258 (tpp) cc_final: 0.7013 (tpp) REVERT: c 409 ASN cc_start: 0.9193 (m-40) cc_final: 0.8723 (m110) REVERT: c 410 MET cc_start: 0.7518 (ttm) cc_final: 0.6584 (ttt) REVERT: c 413 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7620 (tm-30) REVERT: c 418 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8849 (mp0) REVERT: A 116 LYS cc_start: 0.8352 (mmtm) cc_final: 0.7540 (mmmt) REVERT: A 153 MET cc_start: 0.8499 (tmm) cc_final: 0.7929 (tmm) REVERT: A 227 TRP cc_start: 0.8514 (t60) cc_final: 0.8082 (t60) REVERT: A 235 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8235 (ttm-80) REVERT: a 324 GLN cc_start: 0.8433 (tm130) cc_final: 0.7986 (tm-30) REVERT: a 405 GLN cc_start: 0.9217 (tp40) cc_final: 0.8771 (tp-100) REVERT: a 409 ASN cc_start: 0.9189 (m-40) cc_final: 0.8771 (m-40) REVERT: a 413 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7659 (tm-30) REVERT: B 116 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7157 (mmmt) REVERT: B 130 ASP cc_start: 0.8460 (t0) cc_final: 0.7983 (t0) REVERT: b 303 GLU cc_start: 0.8225 (tp30) cc_final: 0.7955 (tp30) REVERT: b 332 MET cc_start: 0.7306 (tpp) cc_final: 0.6968 (tpp) REVERT: b 410 MET cc_start: 0.7766 (ttm) cc_final: 0.7559 (ttm) REVERT: b 414 MET cc_start: 0.8216 (tmm) cc_final: 0.7934 (ttm) REVERT: b 418 GLU cc_start: 0.9199 (tt0) cc_final: 0.8661 (mt-10) outliers start: 22 outliers final: 13 residues processed: 234 average time/residue: 0.2392 time to fit residues: 76.2932 Evaluate side-chains 204 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain c residue 414 MET 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 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain b residue 270 GLU 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 71 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 416 GLN B 90 ASN B 115 HIS B 141 HIS B 209 ASN b 324 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9996 Z= 0.225 Angle : 0.787 9.445 13536 Z= 0.388 Chirality : 0.050 0.406 1743 Planarity : 0.004 0.056 1593 Dihedral : 9.415 52.387 2934 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.80 % Allowed : 13.56 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.12 (0.26), residues: 1074 helix: 0.56 (0.27), residues: 408 sheet: 0.60 (0.45), residues: 126 loop : -0.34 (0.28), 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 179 PHE 0.029 0.002 PHE A 233 TYR 0.020 0.001 TYR A 62 ARG 0.004 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 233 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 1.077 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 66 TYR cc_start: 0.6822 (m-10) cc_final: 0.6325 (m-10) REVERT: C 116 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7654 (mmmt) REVERT: C 130 ASP cc_start: 0.8487 (t0) cc_final: 0.8039 (t0) REVERT: C 153 MET cc_start: 0.8697 (tmm) cc_final: 0.8245 (tmm) REVERT: C 211 ASP cc_start: 0.8809 (m-30) cc_final: 0.8592 (m-30) REVERT: c 332 MET cc_start: 0.7277 (tpp) cc_final: 0.6915 (tpp) REVERT: c 409 ASN cc_start: 0.9207 (m-40) cc_final: 0.8756 (m-40) REVERT: c 410 MET cc_start: 0.7666 (ttm) cc_final: 0.6404 (ttt) REVERT: c 413 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 116 LYS cc_start: 0.8344 (mmtm) cc_final: 0.7856 (mmtt) REVERT: A 153 MET cc_start: 0.8541 (tmm) cc_final: 0.7958 (tmm) REVERT: A 235 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8114 (ttm-80) REVERT: a 321 GLN cc_start: 0.9448 (mm110) cc_final: 0.9086 (mm-40) REVERT: a 341 VAL cc_start: 0.9248 (t) cc_final: 0.9047 (t) REVERT: a 357 ASP cc_start: 0.8731 (t70) cc_final: 0.8425 (t0) REVERT: a 405 GLN cc_start: 0.9236 (tp40) cc_final: 0.9029 (tp-100) REVERT: a 409 ASN cc_start: 0.9172 (m-40) cc_final: 0.8833 (m110) REVERT: a 410 MET cc_start: 0.7796 (ttm) cc_final: 0.7480 (ttm) REVERT: a 413 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 116 LYS cc_start: 0.7778 (mmtt) cc_final: 0.6972 (mmmt) REVERT: B 130 ASP cc_start: 0.8511 (t0) cc_final: 0.8134 (t0) REVERT: B 189 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8570 (mm-40) REVERT: B 235 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.8057 (ttm-80) REVERT: b 303 GLU cc_start: 0.8192 (tp30) cc_final: 0.7888 (tp30) REVERT: b 359 MET cc_start: 0.9158 (tpp) cc_final: 0.8805 (mtp) REVERT: b 410 MET cc_start: 0.7915 (ttm) cc_final: 0.7413 (ttm) REVERT: b 413 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7508 (tm-30) REVERT: b 418 GLU cc_start: 0.9207 (tt0) cc_final: 0.8909 (tm-30) outliers start: 27 outliers final: 14 residues processed: 220 average time/residue: 0.2375 time to fit residues: 71.4746 Evaluate side-chains 207 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 90 ASN 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 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain b residue 270 GLU 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 84 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN A 90 ASN A 189 GLN a 416 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 416 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9996 Z= 0.294 Angle : 0.813 10.103 13536 Z= 0.397 Chirality : 0.050 0.401 1743 Planarity : 0.004 0.077 1593 Dihedral : 9.012 51.940 2934 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.42 % Allowed : 15.73 % 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: -0.09 (0.26), residues: 1074 helix: 0.66 (0.27), residues: 408 sheet: 0.54 (0.53), residues: 96 loop : -0.65 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 386 HIS 0.006 0.001 HIS C 141 PHE 0.018 0.002 PHE A 233 TYR 0.017 0.002 TYR c 278 ARG 0.006 0.001 ARG A 248 *********************** 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 229 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.980 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 66 TYR cc_start: 0.6859 (m-10) cc_final: 0.6324 (m-10) REVERT: C 80 MET cc_start: 0.9124 (tpp) cc_final: 0.8735 (tpp) REVERT: C 116 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7972 (mmmt) REVERT: C 130 ASP cc_start: 0.8609 (t0) cc_final: 0.8093 (t70) REVERT: C 153 MET cc_start: 0.8626 (tmm) cc_final: 0.8149 (tmm) REVERT: C 194 MET cc_start: 0.9029 (tpt) cc_final: 0.8710 (tpt) REVERT: c 410 MET cc_start: 0.7739 (ttm) cc_final: 0.6530 (ttt) REVERT: c 413 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7863 (tm-30) REVERT: c 418 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8165 (mp0) REVERT: A 116 LYS cc_start: 0.8377 (mmtm) cc_final: 0.7810 (mmtt) REVERT: A 153 MET cc_start: 0.8633 (tmm) cc_final: 0.8374 (tmm) REVERT: A 194 MET cc_start: 0.8886 (tpt) cc_final: 0.8657 (tpt) REVERT: a 341 VAL cc_start: 0.9221 (t) cc_final: 0.9020 (t) REVERT: a 410 MET cc_start: 0.7884 (ttm) cc_final: 0.7608 (ttm) REVERT: a 413 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7696 (tm-30) REVERT: B 116 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7112 (mmmt) REVERT: B 130 ASP cc_start: 0.8606 (t0) cc_final: 0.8341 (t0) REVERT: B 235 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.8063 (ttm-80) REVERT: b 303 GLU cc_start: 0.8215 (tp30) cc_final: 0.7802 (tp30) REVERT: b 359 MET cc_start: 0.9310 (tpp) cc_final: 0.8862 (mtt) REVERT: b 410 MET cc_start: 0.8024 (ttm) cc_final: 0.7599 (ttm) REVERT: b 413 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7623 (tm-30) REVERT: b 414 MET cc_start: 0.8356 (tmm) cc_final: 0.7789 (ttm) REVERT: b 418 GLU cc_start: 0.9210 (tt0) cc_final: 0.8703 (mt-10) outliers start: 33 outliers final: 18 residues processed: 214 average time/residue: 0.2333 time to fit residues: 68.3865 Evaluate side-chains 195 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 347 ASP 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 349 LEU 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 270 GLU Chi-restraints excluded: chain b residue 349 LEU 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 34 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 115 HIS C 189 GLN ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN A 185 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9996 Z= 0.209 Angle : 0.763 10.435 13536 Z= 0.374 Chirality : 0.048 0.404 1743 Planarity : 0.003 0.045 1593 Dihedral : 8.521 51.931 2934 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.80 % Allowed : 17.81 % 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: -0.12 (0.26), residues: 1074 helix: 0.59 (0.27), residues: 405 sheet: 0.41 (0.52), residues: 96 loop : -0.61 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.004 0.001 HIS C 93 PHE 0.018 0.001 PHE A 233 TYR 0.017 0.001 TYR b 371 ARG 0.007 0.001 ARG B 248 *********************** 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: 27 poor density : 188 time to evaluate : 1.127 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: 0.6662 (m-10) cc_final: 0.6195 (m-10) REVERT: C 80 MET cc_start: 0.9031 (tpp) cc_final: 0.8724 (tpp) REVERT: C 116 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7583 (mmmt) REVERT: C 130 ASP cc_start: 0.8637 (t0) cc_final: 0.8153 (t0) REVERT: C 153 MET cc_start: 0.8601 (tmm) cc_final: 0.8141 (tmm) REVERT: C 194 MET cc_start: 0.8965 (tpt) cc_final: 0.8732 (tpt) REVERT: C 246 SER cc_start: 0.8504 (p) cc_final: 0.7911 (p) REVERT: c 303 GLU cc_start: 0.7832 (tp30) cc_final: 0.7585 (tp30) REVERT: c 410 MET cc_start: 0.7705 (ttm) cc_final: 0.6512 (ttt) REVERT: c 413 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7872 (tm-30) REVERT: A 116 LYS cc_start: 0.8350 (mmtm) cc_final: 0.7767 (mmtt) REVERT: A 153 MET cc_start: 0.8636 (tmm) cc_final: 0.8394 (tmm) REVERT: a 403 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8079 (tp) REVERT: a 410 MET cc_start: 0.7895 (ttm) cc_final: 0.7585 (ttm) REVERT: a 413 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7701 (tm-30) REVERT: B 116 LYS cc_start: 0.7723 (mmtt) cc_final: 0.6993 (mmmt) REVERT: B 130 ASP cc_start: 0.8523 (t0) cc_final: 0.8312 (t0) REVERT: B 235 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.8158 (ttm-80) REVERT: b 303 GLU cc_start: 0.8163 (tp30) cc_final: 0.7766 (tp30) REVERT: b 405 GLN cc_start: 0.9181 (tp-100) cc_final: 0.8879 (tp40) REVERT: b 410 MET cc_start: 0.8010 (ttm) cc_final: 0.7582 (ttm) REVERT: b 413 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7668 (tm-30) REVERT: b 418 GLU cc_start: 0.9187 (tt0) cc_final: 0.8922 (tm-30) outliers start: 27 outliers final: 14 residues processed: 200 average time/residue: 0.2515 time to fit residues: 68.8862 Evaluate side-chains 194 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 212 CYS 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 349 LEU Chi-restraints excluded: chain a residue 359 MET 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 242 LEU Chi-restraints excluded: chain B residue 247 GLN 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 97 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 101 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN b 335 GLN b 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9996 Z= 0.262 Angle : 0.770 8.812 13536 Z= 0.377 Chirality : 0.048 0.404 1743 Planarity : 0.003 0.044 1593 Dihedral : 8.377 51.968 2934 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.48 % Allowed : 17.81 % Favored : 79.71 % 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: -0.06 (0.26), residues: 1074 helix: 0.86 (0.27), residues: 387 sheet: 0.43 (0.53), residues: 96 loop : -0.71 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 210 HIS 0.005 0.001 HIS C 93 PHE 0.014 0.002 PHE A 233 TYR 0.020 0.001 TYR b 371 ARG 0.010 0.001 ARG B 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 207 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6680 (m-10) cc_final: 0.6369 (m-10) REVERT: C 80 MET cc_start: 0.9168 (tpp) cc_final: 0.8926 (tpp) REVERT: C 116 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7935 (mmmt) REVERT: C 130 ASP cc_start: 0.8655 (t0) cc_final: 0.8236 (t0) REVERT: C 153 MET cc_start: 0.8563 (tmm) cc_final: 0.8066 (tmm) REVERT: C 248 ARG cc_start: 0.7871 (tpt170) cc_final: 0.7464 (tpt170) REVERT: c 410 MET cc_start: 0.7875 (ttm) cc_final: 0.6711 (ttm) REVERT: c 413 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 75 MET cc_start: 0.8949 (mmm) cc_final: 0.8470 (mmt) REVERT: A 153 MET cc_start: 0.8619 (tmm) cc_final: 0.8358 (tmm) REVERT: a 403 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8213 (tp) REVERT: a 410 MET cc_start: 0.7869 (ttm) cc_final: 0.7545 (ttm) REVERT: a 413 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 116 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7152 (mmmt) REVERT: B 235 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.8187 (ttm-80) REVERT: B 248 ARG cc_start: 0.7694 (tpt170) cc_final: 0.6513 (tpm170) REVERT: b 413 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7679 (tm-30) REVERT: b 414 MET cc_start: 0.8343 (tmm) cc_final: 0.7793 (ttm) REVERT: b 418 GLU cc_start: 0.9232 (tt0) cc_final: 0.8765 (mt-10) outliers start: 24 outliers final: 19 residues processed: 198 average time/residue: 0.2470 time to fit residues: 66.4358 Evaluate side-chains 191 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET 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 212 CYS Chi-restraints excluded: chain C residue 249 THR 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 349 LEU Chi-restraints excluded: chain a residue 359 MET 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 242 LEU Chi-restraints excluded: chain B residue 247 GLN 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 40 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9996 Z= 0.297 Angle : 0.801 8.792 13536 Z= 0.390 Chirality : 0.048 0.408 1743 Planarity : 0.004 0.044 1593 Dihedral : 8.398 52.976 2934 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.38 % Allowed : 19.05 % Favored : 78.57 % 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: -0.05 (0.26), residues: 1074 helix: 0.98 (0.28), residues: 387 sheet: 0.44 (0.54), residues: 96 loop : -0.80 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 210 HIS 0.007 0.001 HIS C 93 PHE 0.011 0.002 PHE A 233 TYR 0.026 0.002 TYR a 371 ARG 0.010 0.001 ARG B 248 *********************** 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 203 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6727 (m-10) cc_final: 0.6399 (m-10) REVERT: C 80 MET cc_start: 0.9113 (tpp) cc_final: 0.8807 (tpp) REVERT: C 116 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7939 (mmmt) REVERT: C 130 ASP cc_start: 0.8718 (t0) cc_final: 0.8365 (t0) REVERT: C 153 MET cc_start: 0.8591 (tmm) cc_final: 0.8089 (tmm) REVERT: C 248 ARG cc_start: 0.7907 (tpt170) cc_final: 0.7049 (tpm170) REVERT: c 348 GLN cc_start: 0.8529 (mp10) cc_final: 0.8156 (mt0) REVERT: c 410 MET cc_start: 0.7887 (ttm) cc_final: 0.6766 (ttm) REVERT: c 413 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 116 LYS cc_start: 0.8395 (mmtm) cc_final: 0.7711 (mmtt) REVERT: A 153 MET cc_start: 0.8606 (tmm) cc_final: 0.8308 (tmm) REVERT: a 348 GLN cc_start: 0.8715 (mp10) cc_final: 0.8452 (mt0) REVERT: a 403 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8256 (tp) REVERT: a 410 MET cc_start: 0.8032 (ttm) cc_final: 0.7705 (ttm) REVERT: a 413 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7864 (tm-30) REVERT: B 116 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7195 (mmmt) REVERT: B 235 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8212 (ttm-80) REVERT: B 248 ARG cc_start: 0.7764 (tpt170) cc_final: 0.6816 (tpm170) REVERT: b 335 GLN cc_start: 0.8405 (pm20) cc_final: 0.8091 (pm20) REVERT: b 413 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7694 (tm-30) REVERT: b 414 MET cc_start: 0.8299 (tmm) cc_final: 0.7686 (ttm) REVERT: b 418 GLU cc_start: 0.9229 (tt0) cc_final: 0.8767 (mt-10) outliers start: 23 outliers final: 19 residues processed: 191 average time/residue: 0.2452 time to fit residues: 64.0076 Evaluate side-chains 190 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET 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 212 CYS Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 333 SER 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 359 MET 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 247 GLN Chi-restraints excluded: chain b residue 349 LEU 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 88 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9996 Z= 0.232 Angle : 0.775 7.441 13536 Z= 0.378 Chirality : 0.047 0.404 1743 Planarity : 0.003 0.044 1593 Dihedral : 8.177 53.640 2934 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.17 % Allowed : 19.25 % Favored : 78.57 % 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: 384 sheet: 0.49 (0.56), residues: 96 loop : -0.78 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 210 HIS 0.005 0.001 HIS a 305 PHE 0.013 0.001 PHE A 233 TYR 0.023 0.001 TYR a 371 ARG 0.008 0.001 ARG B 248 *********************** 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 208 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 MET cc_start: 0.9107 (tpp) cc_final: 0.8519 (mpp) REVERT: C 116 LYS cc_start: 0.8225 (mmtt) cc_final: 0.8007 (mmtt) REVERT: C 130 ASP cc_start: 0.8715 (t0) cc_final: 0.8378 (t0) REVERT: C 153 MET cc_start: 0.8549 (tmm) cc_final: 0.8051 (tmm) REVERT: C 248 ARG cc_start: 0.7836 (tpt170) cc_final: 0.6992 (tpm170) REVERT: c 348 GLN cc_start: 0.8465 (mp10) cc_final: 0.8018 (mt0) REVERT: c 413 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 116 LYS cc_start: 0.8390 (mmtm) cc_final: 0.7690 (mmtt) REVERT: A 153 MET cc_start: 0.8601 (tmm) cc_final: 0.8311 (tmm) REVERT: a 347 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7800 (t70) REVERT: a 348 GLN cc_start: 0.8675 (mp10) cc_final: 0.8410 (mt0) REVERT: a 410 MET cc_start: 0.7994 (ttm) cc_final: 0.7648 (ttm) REVERT: a 413 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 116 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7180 (mmmt) REVERT: B 248 ARG cc_start: 0.7673 (tpt170) cc_final: 0.6783 (tpm170) REVERT: b 311 ASP cc_start: 0.8739 (m-30) cc_final: 0.8350 (t0) REVERT: b 410 MET cc_start: 0.8167 (ttm) cc_final: 0.7590 (ttm) REVERT: b 413 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7742 (tm-30) REVERT: b 418 GLU cc_start: 0.9250 (tt0) cc_final: 0.8949 (tm-30) outliers start: 21 outliers final: 19 residues processed: 197 average time/residue: 0.2701 time to fit residues: 73.6768 Evaluate side-chains 194 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET 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 212 CYS Chi-restraints excluded: chain c residue 311 ASP 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 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 359 MET Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN c 324 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9996 Z= 0.211 Angle : 0.780 11.689 13536 Z= 0.380 Chirality : 0.047 0.391 1743 Planarity : 0.004 0.045 1593 Dihedral : 7.965 53.683 2934 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.86 % Allowed : 20.70 % Favored : 77.43 % 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: 1.01 (0.28), residues: 387 sheet: 0.46 (0.57), residues: 96 loop : -0.81 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 210 HIS 0.006 0.001 HIS a 305 PHE 0.013 0.001 PHE A 233 TYR 0.024 0.001 TYR B 62 ARG 0.007 0.001 ARG B 248 ********************** 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 201 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 80 MET cc_start: 0.9087 (tpp) cc_final: 0.8515 (mpp) REVERT: C 116 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7965 (mmtt) REVERT: C 130 ASP cc_start: 0.8655 (t0) cc_final: 0.8265 (t0) REVERT: C 153 MET cc_start: 0.8581 (tmm) cc_final: 0.8109 (tmm) REVERT: C 248 ARG cc_start: 0.7790 (tpt170) cc_final: 0.7089 (tpm170) REVERT: c 348 GLN cc_start: 0.8386 (mp10) cc_final: 0.8075 (mt0) REVERT: c 410 MET cc_start: 0.7730 (ttm) cc_final: 0.6816 (ttt) REVERT: c 413 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7963 (tm-30) REVERT: A 116 LYS cc_start: 0.8381 (mmtm) cc_final: 0.7692 (mmtt) REVERT: A 153 MET cc_start: 0.8573 (tmm) cc_final: 0.8000 (tmm) REVERT: a 347 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7824 (t70) REVERT: a 348 GLN cc_start: 0.8709 (mp10) cc_final: 0.8465 (mt0) REVERT: a 410 MET cc_start: 0.7991 (ttm) cc_final: 0.7629 (ttm) REVERT: a 413 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 66 TYR cc_start: 0.6448 (m-10) cc_final: 0.6171 (m-10) REVERT: B 116 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7186 (mmmt) REVERT: B 247 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: B 248 ARG cc_start: 0.7625 (tpt170) cc_final: 0.6508 (tpm170) REVERT: b 311 ASP cc_start: 0.8698 (m-30) cc_final: 0.8424 (t0) REVERT: b 359 MET cc_start: 0.9166 (tpp) cc_final: 0.8735 (ttt) REVERT: b 410 MET cc_start: 0.8078 (ttm) cc_final: 0.6987 (ttt) REVERT: b 413 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7755 (tm-30) REVERT: b 418 GLU cc_start: 0.9241 (tt0) cc_final: 0.8792 (mt-10) outliers start: 18 outliers final: 15 residues processed: 192 average time/residue: 0.2469 time to fit residues: 64.3803 Evaluate side-chains 190 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 311 ASP 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 359 MET Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0970 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 305 HIS b 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.095855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076455 restraints weight = 27173.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.079071 restraints weight = 16502.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.080865 restraints weight = 12134.569| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9996 Z= 0.218 Angle : 0.785 11.233 13536 Z= 0.383 Chirality : 0.046 0.388 1743 Planarity : 0.004 0.044 1593 Dihedral : 7.917 53.634 2934 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.17 % Allowed : 21.01 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1074 helix: 1.00 (0.27), residues: 387 sheet: 0.26 (0.56), residues: 99 loop : -0.77 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 210 HIS 0.006 0.001 HIS a 305 PHE 0.013 0.001 PHE A 233 TYR 0.029 0.001 TYR B 62 ARG 0.007 0.001 ARG B 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2191.66 seconds wall clock time: 41 minutes 11.44 seconds (2471.44 seconds total)