Starting phenix.real_space_refine on Tue May 13 10:29:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejd_28178/05_2025/8ejd_28178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejd_28178/05_2025/8ejd_28178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejd_28178/05_2025/8ejd_28178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejd_28178/05_2025/8ejd_28178.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejd_28178/05_2025/8ejd_28178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejd_28178/05_2025/8ejd_28178.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 6093 2.51 5 N 1524 2.21 5 O 2094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.19, per 1000 atoms: 0.63 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: 3.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 2.59 Time building geometry restraints manager: 4.01 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: 0.010 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.300 Find NCS groups from input model: 0.430 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.880 ------------------------------------------------------------------------------- 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 10104 Z= 1.202 Angle : 1.929 15.821 13839 Z= 1.142 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 Details of bonding type rmsd link_NAG-ASN : bond 0.07145 ( 33) link_NAG-ASN : angle 3.63699 ( 99) link_ALPHA1-6 : bond 0.05644 ( 9) link_ALPHA1-6 : angle 3.27341 ( 27) link_BETA1-4 : bond 0.07019 ( 39) link_BETA1-4 : angle 5.91989 ( 117) link_ALPHA1-3 : bond 0.00336 ( 3) link_ALPHA1-3 : angle 1.09254 ( 9) hydrogen bonds : bond 0.17915 ( 402) hydrogen bonds : angle 6.44707 ( 1044) link_BETA1-6 : bond 0.06036 ( 3) link_BETA1-6 : angle 3.01618 ( 9) SS BOND : bond 0.00782 ( 21) SS BOND : angle 2.68900 ( 42) covalent geometry : bond 0.02164 ( 9996) covalent geometry : angle 1.83171 (13536) *********************** 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 : 1.055 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: 0.2798 time to fit residues: 131.1953 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 : 1.044 ------------------------------------------------------------------------------- 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: 5.9990 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.1264 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.096670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.075686 restraints weight = 25621.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078618 restraints weight = 14267.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.080693 restraints weight = 10070.688| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10104 Z= 0.216 Angle : 1.085 12.971 13839 Z= 0.507 Chirality : 0.057 0.474 1743 Planarity : 0.005 0.051 1593 Dihedral : 14.561 77.913 2934 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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 : 0.09 % 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: -0.10 (0.25), residues: 1074 helix: 0.05 (0.25), residues: 408 sheet: 1.09 (0.44), residues: 126 loop : -0.33 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP c 386 HIS 0.006 0.001 HIS A 170 PHE 0.014 0.002 PHE B 233 TYR 0.025 0.002 TYR A 62 ARG 0.004 0.001 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 33) link_NAG-ASN : angle 3.49074 ( 99) link_ALPHA1-6 : bond 0.00794 ( 9) link_ALPHA1-6 : angle 1.75905 ( 27) link_BETA1-4 : bond 0.01154 ( 39) link_BETA1-4 : angle 4.60927 ( 117) link_ALPHA1-3 : bond 0.00858 ( 3) link_ALPHA1-3 : angle 1.65370 ( 9) hydrogen bonds : bond 0.06032 ( 402) hydrogen bonds : angle 4.97137 ( 1044) link_BETA1-6 : bond 0.00220 ( 3) link_BETA1-6 : angle 1.71475 ( 9) SS BOND : bond 0.00656 ( 21) SS BOND : angle 2.04285 ( 42) covalent geometry : bond 0.00467 ( 9996) covalent geometry : angle 0.95228 (13536) *********************** 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 267 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 1.086 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: C 62 TYR cc_start: 0.7034 (m-80) cc_final: 0.6442 (m-80) REVERT: C 66 TYR cc_start: 0.6576 (m-80) cc_final: 0.6261 (m-10) REVERT: C 80 MET cc_start: 0.9214 (mmt) cc_final: 0.8781 (tpp) REVERT: C 116 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8029 (mmtt) REVERT: C 130 ASP cc_start: 0.8437 (t0) cc_final: 0.7916 (t0) REVERT: C 189 GLN cc_start: 0.8746 (mt0) cc_final: 0.8498 (mt0) REVERT: C 194 MET cc_start: 0.9116 (tpt) cc_final: 0.8826 (tpt) REVERT: c 321 GLN cc_start: 0.9190 (mm110) cc_final: 0.8796 (mm-40) REVERT: c 332 MET cc_start: 0.7603 (tpp) cc_final: 0.7338 (tpp) REVERT: c 351 MET cc_start: 0.9205 (mmm) cc_final: 0.8931 (mmm) REVERT: c 409 ASN cc_start: 0.9353 (m-40) cc_final: 0.8932 (m-40) REVERT: c 410 MET cc_start: 0.7688 (ttm) cc_final: 0.6597 (ttt) REVERT: c 413 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7517 (tm-30) REVERT: c 417 LYS cc_start: 0.8674 (ptmm) cc_final: 0.8174 (pttt) REVERT: A 116 LYS cc_start: 0.8515 (mmtm) cc_final: 0.7678 (mmmt) REVERT: A 130 ASP cc_start: 0.7974 (t0) cc_final: 0.7685 (t0) REVERT: A 134 MET cc_start: 0.8687 (tpt) cc_final: 0.8472 (tpt) REVERT: A 153 MET cc_start: 0.8275 (tmm) cc_final: 0.7627 (tmm) REVERT: A 194 MET cc_start: 0.9180 (tpp) cc_final: 0.8838 (tpt) REVERT: A 210 TRP cc_start: 0.7707 (t-100) cc_final: 0.7378 (t-100) REVERT: A 227 TRP cc_start: 0.8541 (t60) cc_final: 0.8069 (t60) REVERT: A 235 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7918 (ttm-80) REVERT: a 287 GLU cc_start: 0.7608 (tp30) cc_final: 0.7297 (tp30) REVERT: a 321 GLN cc_start: 0.9315 (mm-40) cc_final: 0.8847 (mm-40) REVERT: a 324 GLN cc_start: 0.8282 (tm130) cc_final: 0.7946 (tm-30) REVERT: a 351 MET cc_start: 0.9050 (tpp) cc_final: 0.8744 (mmm) REVERT: a 401 ASP cc_start: 0.7999 (p0) cc_final: 0.7790 (p0) REVERT: a 405 GLN cc_start: 0.9482 (tp40) cc_final: 0.9052 (tp-100) REVERT: a 409 ASN cc_start: 0.9179 (m-40) cc_final: 0.8879 (m-40) REVERT: a 413 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8001 (tm-30) REVERT: B 66 TYR cc_start: 0.6755 (m-80) cc_final: 0.5895 (m-10) REVERT: B 116 LYS cc_start: 0.8467 (mmtt) cc_final: 0.7714 (mmmt) REVERT: B 130 ASP cc_start: 0.8295 (t0) cc_final: 0.7828 (t0) REVERT: B 134 MET cc_start: 0.8693 (tpt) cc_final: 0.8491 (tpt) REVERT: B 189 GLN cc_start: 0.8765 (mt0) cc_final: 0.8464 (mt0) REVERT: B 210 TRP cc_start: 0.7863 (t-100) cc_final: 0.7530 (t-100) REVERT: B 235 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.8004 (ttm-80) REVERT: b 374 HIS cc_start: 0.8340 (t-90) cc_final: 0.8060 (t-90) REVERT: b 405 GLN cc_start: 0.9470 (tp40) cc_final: 0.9234 (tp-100) REVERT: b 410 MET cc_start: 0.7849 (ttm) cc_final: 0.6808 (ttt) REVERT: b 413 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7418 (tm-30) REVERT: b 417 LYS cc_start: 0.8600 (ptmm) cc_final: 0.8055 (pttt) REVERT: b 420 MET cc_start: 0.7863 (mmt) cc_final: 0.7585 (mmp) outliers start: 28 outliers final: 14 residues processed: 255 average time/residue: 0.2458 time to fit residues: 84.3158 Evaluate side-chains 208 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 242 LEU Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 421 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ** b 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070557 restraints weight = 26515.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.073276 restraints weight = 15216.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075174 restraints weight = 10873.710| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10104 Z= 0.297 Angle : 1.064 11.378 13839 Z= 0.497 Chirality : 0.057 0.428 1743 Planarity : 0.004 0.035 1593 Dihedral : 11.416 57.902 2934 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.70 % Favored : 93.02 % Rotamer: Outliers : 3.11 % Allowed : 12.84 % Favored : 84.06 % 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: -0.05 (0.25), residues: 1074 helix: 0.59 (0.27), residues: 390 sheet: 0.68 (0.45), residues: 126 loop : -0.61 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 386 HIS 0.008 0.002 HIS C 179 PHE 0.019 0.002 PHE C 233 TYR 0.020 0.002 TYR b 393 ARG 0.003 0.001 ARG b 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 33) link_NAG-ASN : angle 3.37172 ( 99) link_ALPHA1-6 : bond 0.00612 ( 9) link_ALPHA1-6 : angle 1.72655 ( 27) link_BETA1-4 : bond 0.00993 ( 39) link_BETA1-4 : angle 3.70404 ( 117) link_ALPHA1-3 : bond 0.00825 ( 3) link_ALPHA1-3 : angle 1.79750 ( 9) hydrogen bonds : bond 0.05461 ( 402) hydrogen bonds : angle 4.68339 ( 1044) link_BETA1-6 : bond 0.00141 ( 3) link_BETA1-6 : angle 2.23684 ( 9) SS BOND : bond 0.00861 ( 21) SS BOND : angle 2.67412 ( 42) covalent geometry : bond 0.00647 ( 9996) covalent geometry : angle 0.96042 (13536) *********************** 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 228 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.152 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: 0.6791 (m-80) cc_final: 0.6244 (m-10) REVERT: C 116 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8151 (mmmt) REVERT: C 130 ASP cc_start: 0.8280 (t0) cc_final: 0.7855 (t0) REVERT: C 153 MET cc_start: 0.8387 (tmm) cc_final: 0.8084 (tmm) REVERT: C 194 MET cc_start: 0.9117 (tpt) cc_final: 0.8810 (tpt) REVERT: C 210 TRP cc_start: 0.7693 (t-100) cc_final: 0.7486 (t-100) REVERT: c 410 MET cc_start: 0.7977 (ttm) cc_final: 0.6707 (ttt) REVERT: A 116 LYS cc_start: 0.8583 (mmtm) cc_final: 0.8364 (mmtp) REVERT: A 130 ASP cc_start: 0.8098 (t0) cc_final: 0.7766 (t70) REVERT: A 153 MET cc_start: 0.8411 (tmm) cc_final: 0.8044 (tmm) REVERT: A 189 GLN cc_start: 0.8772 (mt0) cc_final: 0.8398 (mm-40) REVERT: A 194 MET cc_start: 0.9316 (tpp) cc_final: 0.8923 (tpt) REVERT: a 278 TYR cc_start: 0.8827 (t80) cc_final: 0.8612 (t80) REVERT: a 321 GLN cc_start: 0.9441 (mm-40) cc_final: 0.8888 (mm-40) REVERT: a 324 GLN cc_start: 0.8353 (tm130) cc_final: 0.7613 (tm-30) REVERT: a 374 HIS cc_start: 0.8585 (t-90) cc_final: 0.8292 (t-90) REVERT: a 405 GLN cc_start: 0.9578 (tp40) cc_final: 0.9174 (tp-100) REVERT: a 413 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 116 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7418 (mmmt) REVERT: B 130 ASP cc_start: 0.8464 (t0) cc_final: 0.8017 (t0) REVERT: B 134 MET cc_start: 0.8823 (tpt) cc_final: 0.8417 (tpt) REVERT: B 189 GLN cc_start: 0.8780 (mt0) cc_final: 0.8567 (mt0) REVERT: B 210 TRP cc_start: 0.7721 (t-100) cc_final: 0.7288 (t-100) REVERT: B 235 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8153 (ttm-80) REVERT: b 303 GLU cc_start: 0.7973 (tp30) cc_final: 0.7664 (tp30) REVERT: b 357 ASP cc_start: 0.9195 (t0) cc_final: 0.8959 (t70) REVERT: b 374 HIS cc_start: 0.8542 (t-90) cc_final: 0.8323 (t-90) REVERT: b 405 GLN cc_start: 0.9542 (tp40) cc_final: 0.9328 (tp-100) REVERT: b 410 MET cc_start: 0.8075 (ttm) cc_final: 0.7650 (ttm) REVERT: b 413 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7795 (tm-30) REVERT: b 414 MET cc_start: 0.8231 (tmm) cc_final: 0.7686 (ttm) REVERT: b 418 GLU cc_start: 0.9215 (tt0) cc_final: 0.8757 (mt-10) outliers start: 30 outliers final: 19 residues processed: 215 average time/residue: 0.2228 time to fit residues: 66.4407 Evaluate side-chains 204 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 249 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN a 416 GLN B 90 ASN B 115 HIS b 324 GLN b 416 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.092819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072132 restraints weight = 26232.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.074939 restraints weight = 14845.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076884 restraints weight = 10502.937| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10104 Z= 0.173 Angle : 0.916 11.497 13839 Z= 0.427 Chirality : 0.052 0.424 1743 Planarity : 0.004 0.065 1593 Dihedral : 9.660 52.886 2934 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.69 % Allowed : 13.98 % Favored : 83.33 % 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: -0.17 (0.26), residues: 1074 helix: 0.54 (0.27), residues: 408 sheet: 0.56 (0.45), residues: 126 loop : -0.74 (0.26), 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 0.013 0.002 PHE A 233 TYR 0.018 0.002 TYR B 62 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 33) link_NAG-ASN : angle 3.00752 ( 99) link_ALPHA1-6 : bond 0.00718 ( 9) link_ALPHA1-6 : angle 1.60651 ( 27) link_BETA1-4 : bond 0.00827 ( 39) link_BETA1-4 : angle 3.41165 ( 117) link_ALPHA1-3 : bond 0.01073 ( 3) link_ALPHA1-3 : angle 1.43072 ( 9) hydrogen bonds : bond 0.04559 ( 402) hydrogen bonds : angle 4.32856 ( 1044) link_BETA1-6 : bond 0.00239 ( 3) link_BETA1-6 : angle 1.74522 ( 9) SS BOND : bond 0.00527 ( 21) SS BOND : angle 2.89402 ( 42) covalent geometry : bond 0.00374 ( 9996) covalent geometry : angle 0.81029 (13536) *********************** 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 231 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 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: C 66 TYR cc_start: 0.6611 (m-80) cc_final: 0.6068 (m-10) REVERT: C 80 MET cc_start: 0.9097 (mmt) cc_final: 0.8148 (tpp) REVERT: C 116 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8156 (mmmt) REVERT: C 130 ASP cc_start: 0.8269 (t0) cc_final: 0.7680 (t70) REVERT: C 153 MET cc_start: 0.8554 (tmm) cc_final: 0.7935 (tmm) REVERT: C 189 GLN cc_start: 0.8898 (mt0) cc_final: 0.8563 (mm-40) REVERT: C 194 MET cc_start: 0.9137 (tpt) cc_final: 0.8930 (tpt) REVERT: C 211 ASP cc_start: 0.9093 (m-30) cc_final: 0.8883 (m-30) REVERT: c 287 GLU cc_start: 0.8073 (tp30) cc_final: 0.7550 (tp30) REVERT: c 410 MET cc_start: 0.7932 (ttm) cc_final: 0.6709 (ttt) REVERT: A 96 MET cc_start: 0.7911 (mmm) cc_final: 0.7318 (mtp) REVERT: A 116 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8340 (mmtp) REVERT: A 130 ASP cc_start: 0.8110 (t0) cc_final: 0.7789 (t70) REVERT: A 153 MET cc_start: 0.8536 (tmm) cc_final: 0.8128 (tmm) REVERT: A 189 GLN cc_start: 0.8781 (mt0) cc_final: 0.8250 (mm-40) REVERT: A 194 MET cc_start: 0.9259 (tpp) cc_final: 0.8918 (tpt) REVERT: A 235 ARG cc_start: 0.8392 (ttm-80) cc_final: 0.7819 (ttm-80) REVERT: a 357 ASP cc_start: 0.9093 (t70) cc_final: 0.8689 (t70) REVERT: a 374 HIS cc_start: 0.8511 (t-90) cc_final: 0.8130 (t-90) REVERT: a 405 GLN cc_start: 0.9570 (tp40) cc_final: 0.9354 (tp-100) REVERT: a 413 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 75 MET cc_start: 0.7760 (mtm) cc_final: 0.7479 (mtm) REVERT: B 90 ASN cc_start: 0.7171 (OUTLIER) cc_final: 0.6829 (t0) REVERT: B 116 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7427 (mmmt) REVERT: B 130 ASP cc_start: 0.8466 (t0) cc_final: 0.7970 (t0) REVERT: B 189 GLN cc_start: 0.8781 (mt0) cc_final: 0.8437 (mt0) REVERT: B 210 TRP cc_start: 0.7667 (t-100) cc_final: 0.7125 (t-100) REVERT: B 235 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.8064 (ttm-80) REVERT: b 303 GLU cc_start: 0.8021 (tp30) cc_final: 0.7716 (tp30) REVERT: b 357 ASP cc_start: 0.9148 (t0) cc_final: 0.8897 (t70) REVERT: b 374 HIS cc_start: 0.8378 (t-90) cc_final: 0.7930 (t-90) REVERT: b 405 GLN cc_start: 0.9531 (tp40) cc_final: 0.9235 (tp40) REVERT: b 409 ASN cc_start: 0.9447 (m-40) cc_final: 0.9154 (m-40) REVERT: b 418 GLU cc_start: 0.9206 (tt0) cc_final: 0.8969 (tm-30) outliers start: 26 outliers final: 13 residues processed: 216 average time/residue: 0.2387 time to fit residues: 70.0814 Evaluate side-chains 194 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 204 ASP 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 180 CYS Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 90 ASN 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 30 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 63 optimal weight: 0.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN B 90 ASN b 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.093098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072191 restraints weight = 27106.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075026 restraints weight = 15556.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.076967 restraints weight = 11128.043| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10104 Z= 0.160 Angle : 0.884 10.474 13839 Z= 0.410 Chirality : 0.050 0.420 1743 Planarity : 0.004 0.101 1593 Dihedral : 9.092 52.634 2934 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.17 % Allowed : 16.25 % Favored : 81.57 % 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: -0.19 (0.26), residues: 1074 helix: 0.70 (0.27), residues: 405 sheet: 0.77 (0.53), residues: 96 loop : -0.89 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 386 HIS 0.004 0.001 HIS c 305 PHE 0.012 0.001 PHE C 233 TYR 0.021 0.002 TYR C 62 ARG 0.006 0.000 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 33) link_NAG-ASN : angle 2.96797 ( 99) link_ALPHA1-6 : bond 0.00694 ( 9) link_ALPHA1-6 : angle 1.55724 ( 27) link_BETA1-4 : bond 0.00811 ( 39) link_BETA1-4 : angle 3.21302 ( 117) link_ALPHA1-3 : bond 0.01123 ( 3) link_ALPHA1-3 : angle 1.39465 ( 9) hydrogen bonds : bond 0.04316 ( 402) hydrogen bonds : angle 4.24186 ( 1044) link_BETA1-6 : bond 0.00283 ( 3) link_BETA1-6 : angle 1.61228 ( 9) SS BOND : bond 0.00556 ( 21) SS BOND : angle 2.92269 ( 42) covalent geometry : bond 0.00347 ( 9996) covalent geometry : angle 0.78123 (13536) *********************** 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 214 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6506 (m-80) cc_final: 0.5832 (m-10) REVERT: C 116 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8160 (mmmt) REVERT: C 130 ASP cc_start: 0.8432 (t0) cc_final: 0.7794 (t70) REVERT: C 153 MET cc_start: 0.8525 (tmm) cc_final: 0.7873 (tmm) REVERT: C 185 ASN cc_start: 0.7482 (t0) cc_final: 0.6991 (t0) REVERT: c 410 MET cc_start: 0.7958 (ttm) cc_final: 0.6648 (ttt) REVERT: A 96 MET cc_start: 0.7780 (mmm) cc_final: 0.7233 (mtp) REVERT: A 116 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8385 (mmtp) REVERT: A 130 ASP cc_start: 0.8009 (t0) cc_final: 0.7658 (t70) REVERT: A 153 MET cc_start: 0.8542 (tmm) cc_final: 0.8130 (tmm) REVERT: A 189 GLN cc_start: 0.8706 (mt0) cc_final: 0.8134 (mm-40) REVERT: A 194 MET cc_start: 0.9287 (tpp) cc_final: 0.8903 (tpt) REVERT: A 214 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8495 (mtm) REVERT: A 235 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.7809 (ttm-80) REVERT: a 357 ASP cc_start: 0.9070 (t70) cc_final: 0.8648 (t70) REVERT: a 374 HIS cc_start: 0.8391 (t-90) cc_final: 0.8045 (t-90) REVERT: a 405 GLN cc_start: 0.9584 (tp40) cc_final: 0.9368 (tp-100) REVERT: a 410 MET cc_start: 0.8127 (ttm) cc_final: 0.7885 (ttm) REVERT: a 413 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8287 (tm-30) REVERT: B 66 TYR cc_start: 0.6630 (m-80) cc_final: 0.6057 (m-10) REVERT: B 75 MET cc_start: 0.7829 (mtm) cc_final: 0.7572 (mtm) REVERT: B 116 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7489 (mmmt) REVERT: B 122 ASP cc_start: 0.9383 (m-30) cc_final: 0.9116 (m-30) REVERT: B 130 ASP cc_start: 0.8396 (t0) cc_final: 0.7972 (t0) REVERT: B 134 MET cc_start: 0.8530 (mmm) cc_final: 0.8206 (tmm) REVERT: B 189 GLN cc_start: 0.8789 (mt0) cc_final: 0.7726 (mt0) REVERT: B 210 TRP cc_start: 0.7570 (t-100) cc_final: 0.6538 (t-100) REVERT: b 303 GLU cc_start: 0.8041 (tp30) cc_final: 0.7683 (tp30) REVERT: b 357 ASP cc_start: 0.9127 (t0) cc_final: 0.8886 (t70) REVERT: b 374 HIS cc_start: 0.8456 (t-90) cc_final: 0.8205 (t-90) REVERT: b 405 GLN cc_start: 0.9517 (tp40) cc_final: 0.9208 (tp-100) REVERT: b 409 ASN cc_start: 0.9447 (m-40) cc_final: 0.9192 (m110) REVERT: b 410 MET cc_start: 0.8080 (ttm) cc_final: 0.6909 (ttt) REVERT: b 413 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7979 (tm-30) REVERT: b 414 MET cc_start: 0.8088 (tmm) cc_final: 0.7623 (ttm) REVERT: b 418 GLU cc_start: 0.9164 (tt0) cc_final: 0.8741 (mt-10) outliers start: 21 outliers final: 13 residues processed: 204 average time/residue: 0.2467 time to fit residues: 67.9617 Evaluate side-chains 197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 324 GLN c 335 GLN c 416 GLN A 90 ASN ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.094165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074677 restraints weight = 27710.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077218 restraints weight = 16925.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078993 restraints weight = 12508.441| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10104 Z= 0.168 Angle : 0.861 10.569 13839 Z= 0.399 Chirality : 0.049 0.417 1743 Planarity : 0.004 0.045 1593 Dihedral : 8.726 52.333 2934 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.00 % Allowed : 17.08 % Favored : 79.92 % 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: -0.20 (0.26), residues: 1074 helix: 0.72 (0.27), residues: 405 sheet: 0.76 (0.54), residues: 96 loop : -0.91 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 386 HIS 0.005 0.001 HIS C 93 PHE 0.009 0.001 PHE a 399 TYR 0.025 0.001 TYR B 62 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 33) link_NAG-ASN : angle 2.95136 ( 99) link_ALPHA1-6 : bond 0.00662 ( 9) link_ALPHA1-6 : angle 1.52115 ( 27) link_BETA1-4 : bond 0.00746 ( 39) link_BETA1-4 : angle 3.12390 ( 117) link_ALPHA1-3 : bond 0.01075 ( 3) link_ALPHA1-3 : angle 1.33578 ( 9) hydrogen bonds : bond 0.04215 ( 402) hydrogen bonds : angle 4.17074 ( 1044) link_BETA1-6 : bond 0.00221 ( 3) link_BETA1-6 : angle 1.61645 ( 9) SS BOND : bond 0.00419 ( 21) SS BOND : angle 2.34533 ( 42) covalent geometry : bond 0.00370 ( 9996) covalent geometry : angle 0.76505 (13536) *********************** 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 222 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6524 (m-80) cc_final: 0.5767 (m-10) REVERT: C 116 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7958 (mmtt) REVERT: C 130 ASP cc_start: 0.8605 (t0) cc_final: 0.8144 (t0) REVERT: C 153 MET cc_start: 0.8546 (tmm) cc_final: 0.7943 (tmm) REVERT: C 211 ASP cc_start: 0.8788 (m-30) cc_final: 0.8473 (m-30) REVERT: C 246 SER cc_start: 0.8669 (p) cc_final: 0.8196 (p) REVERT: c 287 GLU cc_start: 0.7682 (tp30) cc_final: 0.7362 (tp30) REVERT: c 410 MET cc_start: 0.8012 (ttm) cc_final: 0.6667 (ttt) REVERT: A 96 MET cc_start: 0.7557 (mmm) cc_final: 0.7289 (mtp) REVERT: A 130 ASP cc_start: 0.8163 (t0) cc_final: 0.7854 (t70) REVERT: A 153 MET cc_start: 0.8519 (tmm) cc_final: 0.8156 (tmm) REVERT: A 189 GLN cc_start: 0.8720 (mt0) cc_final: 0.8300 (mt0) REVERT: A 194 MET cc_start: 0.9192 (tpp) cc_final: 0.8943 (tpt) REVERT: A 235 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.7900 (ttm-80) REVERT: a 335 GLN cc_start: 0.8632 (pm20) cc_final: 0.8303 (pm20) REVERT: a 341 VAL cc_start: 0.9303 (t) cc_final: 0.9082 (t) REVERT: a 348 GLN cc_start: 0.8688 (mp10) cc_final: 0.8387 (mt0) REVERT: a 357 ASP cc_start: 0.8968 (t70) cc_final: 0.8621 (t70) REVERT: a 374 HIS cc_start: 0.8201 (t-90) cc_final: 0.7948 (t-90) REVERT: a 410 MET cc_start: 0.8180 (ttm) cc_final: 0.7921 (ttm) REVERT: a 413 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8256 (tm-30) REVERT: B 66 TYR cc_start: 0.6648 (m-80) cc_final: 0.6125 (m-10) REVERT: B 116 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7171 (mmmt) REVERT: B 122 ASP cc_start: 0.9154 (m-30) cc_final: 0.8906 (m-30) REVERT: B 130 ASP cc_start: 0.8607 (t0) cc_final: 0.8256 (t0) REVERT: B 189 GLN cc_start: 0.8680 (mt0) cc_final: 0.8407 (mm-40) REVERT: B 235 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8059 (ttm-80) REVERT: b 303 GLU cc_start: 0.8054 (tp30) cc_final: 0.7723 (tp30) REVERT: b 357 ASP cc_start: 0.9101 (t0) cc_final: 0.8889 (t70) REVERT: b 410 MET cc_start: 0.8122 (ttm) cc_final: 0.7195 (ttt) REVERT: b 418 GLU cc_start: 0.9117 (tt0) cc_final: 0.8900 (tm-30) outliers start: 29 outliers final: 16 residues processed: 207 average time/residue: 0.2389 time to fit residues: 66.9167 Evaluate side-chains 197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 189 GLN 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 402 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.094545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074615 restraints weight = 27896.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077186 restraints weight = 16898.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.079007 restraints weight = 12438.599| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10104 Z= 0.162 Angle : 0.852 10.483 13839 Z= 0.392 Chirality : 0.048 0.420 1743 Planarity : 0.004 0.046 1593 Dihedral : 8.440 52.268 2934 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.59 % Allowed : 17.70 % 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: -0.19 (0.26), residues: 1074 helix: 0.71 (0.27), residues: 405 sheet: 0.79 (0.54), residues: 96 loop : -0.90 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 386 HIS 0.005 0.001 HIS c 305 PHE 0.017 0.001 PHE B 233 TYR 0.027 0.001 TYR B 62 ARG 0.007 0.001 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 33) link_NAG-ASN : angle 2.88955 ( 99) link_ALPHA1-6 : bond 0.00653 ( 9) link_ALPHA1-6 : angle 1.48959 ( 27) link_BETA1-4 : bond 0.00752 ( 39) link_BETA1-4 : angle 3.04609 ( 117) link_ALPHA1-3 : bond 0.01058 ( 3) link_ALPHA1-3 : angle 1.20806 ( 9) hydrogen bonds : bond 0.04089 ( 402) hydrogen bonds : angle 4.20075 ( 1044) link_BETA1-6 : bond 0.00166 ( 3) link_BETA1-6 : angle 1.50771 ( 9) SS BOND : bond 0.00413 ( 21) SS BOND : angle 1.49460 ( 42) covalent geometry : bond 0.00361 ( 9996) covalent geometry : angle 0.76603 (13536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6394 (m-80) cc_final: 0.5753 (m-10) REVERT: C 116 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7876 (mmmt) REVERT: C 130 ASP cc_start: 0.8564 (t0) cc_final: 0.8064 (t0) REVERT: C 153 MET cc_start: 0.8525 (tmm) cc_final: 0.7925 (tmm) REVERT: C 194 MET cc_start: 0.9066 (tpt) cc_final: 0.8734 (tpt) REVERT: C 248 ARG cc_start: 0.8340 (tpt170) cc_final: 0.7164 (tpm170) REVERT: c 401 ASP cc_start: 0.7682 (p0) cc_final: 0.7456 (p0) REVERT: c 410 MET cc_start: 0.8021 (ttm) cc_final: 0.6681 (ttt) REVERT: A 96 MET cc_start: 0.7532 (mmm) cc_final: 0.7223 (mtp) REVERT: A 116 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8030 (mmtp) REVERT: A 130 ASP cc_start: 0.8155 (t0) cc_final: 0.7812 (t70) REVERT: A 153 MET cc_start: 0.8523 (tmm) cc_final: 0.8136 (tmm) REVERT: A 189 GLN cc_start: 0.8721 (mt0) cc_final: 0.8273 (mt0) REVERT: A 194 MET cc_start: 0.9198 (tpp) cc_final: 0.8898 (tpt) REVERT: A 235 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7921 (ttm-80) REVERT: a 357 ASP cc_start: 0.8989 (t70) cc_final: 0.8608 (t70) REVERT: a 374 HIS cc_start: 0.8242 (t-90) cc_final: 0.8037 (t-90) REVERT: a 410 MET cc_start: 0.8188 (ttm) cc_final: 0.7038 (ttt) REVERT: a 413 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 66 TYR cc_start: 0.6556 (m-80) cc_final: 0.6102 (m-10) REVERT: B 116 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7179 (mmmt) REVERT: B 122 ASP cc_start: 0.9250 (m-30) cc_final: 0.9003 (m-30) REVERT: B 130 ASP cc_start: 0.8577 (t0) cc_final: 0.8235 (t0) REVERT: B 189 GLN cc_start: 0.8753 (mt0) cc_final: 0.8427 (mm-40) REVERT: B 248 ARG cc_start: 0.7757 (tpt170) cc_final: 0.7350 (tpm170) REVERT: b 410 MET cc_start: 0.8082 (ttm) cc_final: 0.6933 (ttt) REVERT: b 413 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7965 (tm-30) REVERT: b 414 MET cc_start: 0.8054 (tmm) cc_final: 0.7568 (ttm) REVERT: b 418 GLU cc_start: 0.9201 (tt0) cc_final: 0.8803 (mt-10) outliers start: 25 outliers final: 18 residues processed: 197 average time/residue: 0.2450 time to fit residues: 65.4305 Evaluate side-chains 194 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 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 349 LEU Chi-restraints excluded: chain a residue 359 MET Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 88 optimal weight: 0.0030 chunk 13 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 189 GLN A 90 ASN B 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.095312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075556 restraints weight = 27798.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.078149 restraints weight = 16905.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.080019 restraints weight = 12443.888| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10104 Z= 0.144 Angle : 0.826 9.905 13839 Z= 0.382 Chirality : 0.047 0.412 1743 Planarity : 0.004 0.058 1593 Dihedral : 8.062 53.099 2934 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.17 % Allowed : 17.91 % Favored : 79.92 % 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: 1.06 (0.28), residues: 384 sheet: 0.84 (0.56), residues: 96 loop : -0.84 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 386 HIS 0.004 0.001 HIS a 305 PHE 0.021 0.001 PHE B 233 TYR 0.026 0.001 TYR B 62 ARG 0.007 0.001 ARG C 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 33) link_NAG-ASN : angle 2.78806 ( 99) link_ALPHA1-6 : bond 0.00650 ( 9) link_ALPHA1-6 : angle 1.42122 ( 27) link_BETA1-4 : bond 0.00736 ( 39) link_BETA1-4 : angle 2.95488 ( 117) link_ALPHA1-3 : bond 0.01053 ( 3) link_ALPHA1-3 : angle 1.13660 ( 9) hydrogen bonds : bond 0.03914 ( 402) hydrogen bonds : angle 4.13597 ( 1044) link_BETA1-6 : bond 0.00294 ( 3) link_BETA1-6 : angle 1.44557 ( 9) SS BOND : bond 0.00269 ( 21) SS BOND : angle 1.23622 ( 42) covalent geometry : bond 0.00312 ( 9996) covalent geometry : angle 0.74476 (13536) *********************** 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 214 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 1.037 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: 0.6217 (m-80) cc_final: 0.5659 (m-10) REVERT: C 116 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7779 (mmmt) REVERT: C 130 ASP cc_start: 0.8552 (t0) cc_final: 0.8018 (t0) REVERT: C 153 MET cc_start: 0.8527 (tmm) cc_final: 0.7978 (tmm) REVERT: C 194 MET cc_start: 0.9048 (tpt) cc_final: 0.8667 (tpt) REVERT: C 248 ARG cc_start: 0.8316 (tpt170) cc_final: 0.7216 (tpm170) REVERT: c 405 GLN cc_start: 0.9250 (tp-100) cc_final: 0.8837 (tp-100) REVERT: c 410 MET cc_start: 0.8042 (ttm) cc_final: 0.6719 (ttt) REVERT: A 66 TYR cc_start: 0.6139 (m-10) cc_final: 0.5509 (m-10) REVERT: A 116 LYS cc_start: 0.8351 (mmtm) cc_final: 0.7957 (mmtp) REVERT: A 130 ASP cc_start: 0.8130 (t0) cc_final: 0.7812 (t70) REVERT: A 153 MET cc_start: 0.8526 (tmm) cc_final: 0.7829 (tmm) REVERT: A 189 GLN cc_start: 0.8742 (mt0) cc_final: 0.8302 (mm-40) REVERT: A 194 MET cc_start: 0.9135 (tpp) cc_final: 0.8866 (tpt) REVERT: A 235 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7930 (ttm-80) REVERT: a 351 MET cc_start: 0.9134 (tpp) cc_final: 0.8870 (mmm) REVERT: a 357 ASP cc_start: 0.8903 (t70) cc_final: 0.8561 (t70) REVERT: a 374 HIS cc_start: 0.8153 (t-90) cc_final: 0.7742 (t-90) REVERT: a 410 MET cc_start: 0.8203 (ttm) cc_final: 0.7078 (ttm) REVERT: a 413 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8249 (tm-30) REVERT: B 116 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7155 (mmmt) REVERT: B 130 ASP cc_start: 0.8581 (t0) cc_final: 0.8266 (t0) REVERT: B 134 MET cc_start: 0.8365 (tpt) cc_final: 0.8081 (tmm) REVERT: B 189 GLN cc_start: 0.8693 (mt0) cc_final: 0.8401 (mm-40) REVERT: B 247 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8216 (pm20) REVERT: B 248 ARG cc_start: 0.8008 (tpt170) cc_final: 0.7152 (tpm170) REVERT: b 311 ASP cc_start: 0.8947 (m-30) cc_final: 0.8460 (t0) REVERT: b 374 HIS cc_start: 0.8221 (t-90) cc_final: 0.7947 (t-90) REVERT: b 413 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7887 (tm-30) REVERT: b 418 GLU cc_start: 0.9155 (tt0) cc_final: 0.8911 (tm-30) outliers start: 21 outliers final: 15 residues processed: 202 average time/residue: 0.2497 time to fit residues: 68.3327 Evaluate side-chains 194 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 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 359 MET Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 403 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN b 335 GLN b 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.093880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.074195 restraints weight = 27738.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076715 restraints weight = 17183.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.078506 restraints weight = 12708.516| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10104 Z= 0.187 Angle : 0.857 9.835 13839 Z= 0.397 Chirality : 0.048 0.413 1743 Planarity : 0.004 0.045 1593 Dihedral : 8.064 53.434 2934 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.69 % Allowed : 18.53 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1074 helix: 1.05 (0.28), residues: 387 sheet: 0.82 (0.55), residues: 96 loop : -0.85 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 386 HIS 0.005 0.001 HIS C 93 PHE 0.016 0.001 PHE B 233 TYR 0.032 0.002 TYR C 62 ARG 0.008 0.001 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 33) link_NAG-ASN : angle 2.91244 ( 99) link_ALPHA1-6 : bond 0.00599 ( 9) link_ALPHA1-6 : angle 1.51009 ( 27) link_BETA1-4 : bond 0.00717 ( 39) link_BETA1-4 : angle 2.95040 ( 117) link_ALPHA1-3 : bond 0.00914 ( 3) link_ALPHA1-3 : angle 1.27955 ( 9) hydrogen bonds : bond 0.04063 ( 402) hydrogen bonds : angle 4.20185 ( 1044) link_BETA1-6 : bond 0.00151 ( 3) link_BETA1-6 : angle 1.61737 ( 9) SS BOND : bond 0.00314 ( 21) SS BOND : angle 1.35153 ( 42) covalent geometry : bond 0.00420 ( 9996) covalent geometry : angle 0.77506 (13536) *********************** 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 209 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6410 (m-80) cc_final: 0.5787 (m-10) REVERT: C 116 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7699 (mmmt) REVERT: C 130 ASP cc_start: 0.8627 (t0) cc_final: 0.8148 (t0) REVERT: C 153 MET cc_start: 0.8566 (tmm) cc_final: 0.7990 (tmm) REVERT: C 192 MET cc_start: 0.8706 (tpp) cc_final: 0.8479 (mmt) REVERT: C 194 MET cc_start: 0.9032 (tpt) cc_final: 0.8715 (tpt) REVERT: C 248 ARG cc_start: 0.8301 (tpt170) cc_final: 0.7437 (tpm170) REVERT: c 405 GLN cc_start: 0.9251 (tp-100) cc_final: 0.8846 (tp-100) REVERT: c 410 MET cc_start: 0.8088 (ttm) cc_final: 0.6737 (ttt) REVERT: A 75 MET cc_start: 0.9268 (mmm) cc_final: 0.8995 (mmt) REVERT: A 116 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8016 (mmtp) REVERT: A 130 ASP cc_start: 0.8152 (t0) cc_final: 0.7795 (t70) REVERT: A 153 MET cc_start: 0.8537 (tmm) cc_final: 0.7845 (tmm) REVERT: A 194 MET cc_start: 0.9128 (tpp) cc_final: 0.8869 (tpt) REVERT: A 235 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.7987 (ttm-80) REVERT: a 351 MET cc_start: 0.9146 (tpp) cc_final: 0.8891 (mmm) REVERT: a 357 ASP cc_start: 0.8958 (t70) cc_final: 0.8645 (t70) REVERT: a 374 HIS cc_start: 0.8192 (t-90) cc_final: 0.7768 (t-90) REVERT: a 405 GLN cc_start: 0.9331 (tp-100) cc_final: 0.8988 (tp-100) REVERT: a 413 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 66 TYR cc_start: 0.6539 (m-80) cc_final: 0.6194 (m-10) REVERT: B 116 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7083 (mmmt) REVERT: B 130 ASP cc_start: 0.8657 (t0) cc_final: 0.8395 (t0) REVERT: B 189 GLN cc_start: 0.8693 (mt0) cc_final: 0.8383 (mt0) REVERT: B 248 ARG cc_start: 0.8188 (tpt170) cc_final: 0.7574 (tpm170) REVERT: b 311 ASP cc_start: 0.8993 (m-30) cc_final: 0.8530 (t0) REVERT: b 348 GLN cc_start: 0.8457 (mp10) cc_final: 0.8117 (mt0) REVERT: b 410 MET cc_start: 0.8081 (ttm) cc_final: 0.7121 (ttt) REVERT: b 414 MET cc_start: 0.8100 (tmm) cc_final: 0.7704 (ttm) REVERT: b 418 GLU cc_start: 0.9161 (tt0) cc_final: 0.8703 (mt-10) outliers start: 26 outliers final: 21 residues processed: 197 average time/residue: 0.2408 time to fit residues: 64.4507 Evaluate side-chains 199 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 292 CYS 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 421 GLU Chi-restraints excluded: chain B residue 82 MET 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 347 ASP Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 403 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 79 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.0270 chunk 28 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.096327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.076950 restraints weight = 27452.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.079558 restraints weight = 16829.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.081451 restraints weight = 12339.383| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10104 Z= 0.141 Angle : 0.835 9.673 13839 Z= 0.389 Chirality : 0.046 0.405 1743 Planarity : 0.004 0.047 1593 Dihedral : 7.757 53.387 2934 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.97 % Allowed : 19.67 % Favored : 78.36 % 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: 1.10 (0.28), residues: 387 sheet: 0.70 (0.58), residues: 90 loop : -0.79 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 210 HIS 0.006 0.001 HIS c 305 PHE 0.019 0.001 PHE B 233 TYR 0.028 0.001 TYR C 62 ARG 0.008 0.001 ARG A 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 33) link_NAG-ASN : angle 2.67578 ( 99) link_ALPHA1-6 : bond 0.00665 ( 9) link_ALPHA1-6 : angle 1.35502 ( 27) link_BETA1-4 : bond 0.00771 ( 39) link_BETA1-4 : angle 2.87191 ( 117) link_ALPHA1-3 : bond 0.01067 ( 3) link_ALPHA1-3 : angle 1.07145 ( 9) hydrogen bonds : bond 0.03823 ( 402) hydrogen bonds : angle 4.27903 ( 1044) link_BETA1-6 : bond 0.00353 ( 3) link_BETA1-6 : angle 1.37021 ( 9) SS BOND : bond 0.00238 ( 21) SS BOND : angle 1.16576 ( 42) covalent geometry : bond 0.00305 ( 9996) covalent geometry : angle 0.76086 (13536) ********************** 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 211 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7433 (mmmt) REVERT: C 130 ASP cc_start: 0.8538 (t0) cc_final: 0.8003 (t0) REVERT: C 153 MET cc_start: 0.8516 (tmm) cc_final: 0.7983 (tmm) REVERT: C 194 MET cc_start: 0.9008 (tpt) cc_final: 0.8725 (tpt) REVERT: c 405 GLN cc_start: 0.9261 (tp-100) cc_final: 0.8888 (tp-100) REVERT: A 116 LYS cc_start: 0.8338 (mmtm) cc_final: 0.8006 (mmtp) REVERT: A 130 ASP cc_start: 0.8156 (t0) cc_final: 0.7825 (t70) REVERT: A 153 MET cc_start: 0.8437 (tmm) cc_final: 0.7727 (tmm) REVERT: A 194 MET cc_start: 0.9129 (tpp) cc_final: 0.8892 (tpt) REVERT: A 235 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.7976 (ttm-80) REVERT: a 351 MET cc_start: 0.9111 (tpp) cc_final: 0.8810 (mmm) REVERT: a 357 ASP cc_start: 0.8885 (t70) cc_final: 0.8664 (t70) REVERT: a 374 HIS cc_start: 0.8088 (t-90) cc_final: 0.7734 (t-90) REVERT: a 400 SER cc_start: 0.8235 (t) cc_final: 0.7975 (p) REVERT: a 410 MET cc_start: 0.8139 (ttm) cc_final: 0.7151 (ttm) REVERT: a 413 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 116 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7137 (mtpt) REVERT: B 130 ASP cc_start: 0.8603 (t0) cc_final: 0.8373 (t0) REVERT: B 248 ARG cc_start: 0.7544 (tpt170) cc_final: 0.6856 (tpm170) REVERT: B 250 ARG cc_start: 0.7486 (mmt180) cc_final: 0.7005 (mmt180) REVERT: b 311 ASP cc_start: 0.8898 (m-30) cc_final: 0.8451 (t0) REVERT: b 332 MET cc_start: 0.7655 (tpp) cc_final: 0.7092 (tpt) REVERT: b 414 MET cc_start: 0.8192 (tmm) cc_final: 0.7653 (ttm) REVERT: b 418 GLU cc_start: 0.9161 (tt0) cc_final: 0.8698 (mt-10) outliers start: 19 outliers final: 14 residues processed: 200 average time/residue: 0.2319 time to fit residues: 62.5821 Evaluate side-chains 189 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET 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 359 MET Chi-restraints excluded: chain c residue 402 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 82 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 403 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 209 ASN A 90 ASN a 331 GLN ** a 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.093206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073389 restraints weight = 27326.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075850 restraints weight = 16707.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077549 restraints weight = 12368.933| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10104 Z= 0.238 Angle : 0.929 10.731 13839 Z= 0.431 Chirality : 0.049 0.410 1743 Planarity : 0.004 0.044 1593 Dihedral : 8.142 53.818 2934 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 1.97 % Allowed : 20.70 % Favored : 77.33 % 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: -0.11 (0.26), residues: 1074 helix: 0.98 (0.27), residues: 387 sheet: 0.50 (0.57), residues: 90 loop : -0.88 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 210 HIS 0.007 0.001 HIS B 141 PHE 0.014 0.002 PHE B 157 TYR 0.025 0.002 TYR A 66 ARG 0.016 0.001 ARG C 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 33) link_NAG-ASN : angle 3.00957 ( 99) link_ALPHA1-6 : bond 0.00590 ( 9) link_ALPHA1-6 : angle 1.66759 ( 27) link_BETA1-4 : bond 0.00693 ( 39) link_BETA1-4 : angle 2.95611 ( 117) link_ALPHA1-3 : bond 0.00609 ( 3) link_ALPHA1-3 : angle 1.51633 ( 9) hydrogen bonds : bond 0.04332 ( 402) hydrogen bonds : angle 4.36736 ( 1044) link_BETA1-6 : bond 0.00011 ( 3) link_BETA1-6 : angle 1.76977 ( 9) SS BOND : bond 0.00425 ( 21) SS BOND : angle 1.61116 ( 42) covalent geometry : bond 0.00535 ( 9996) covalent geometry : angle 0.85099 (13536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3130.67 seconds wall clock time: 56 minutes 7.28 seconds (3367.28 seconds total)