Starting phenix.real_space_refine on Fri Jan 17 07:13:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vcv_43141/01_2025/8vcv_43141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vcv_43141/01_2025/8vcv_43141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vcv_43141/01_2025/8vcv_43141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vcv_43141/01_2025/8vcv_43141.map" model { file = "/net/cci-nas-00/data/ceres_data/8vcv_43141/01_2025/8vcv_43141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vcv_43141/01_2025/8vcv_43141.cif" } resolution = 2.8 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= -0.000 sd= 0.019 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 87 5.16 5 C 6498 2.51 5 N 1696 2.21 5 O 2185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10466 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 625 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 550 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 110 Planarities with less than four sites: {'UNK:plan-1': 110} Unresolved non-hydrogen planarities: 110 Chain: "a" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "b" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "c" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: "S" 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: "T" 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: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.50, per 1000 atoms: 1.29 Number of scatterers: 10466 At special positions: 0 Unit cell: (108.418, 109.136, 96.212, 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 87 16.00 O 2185 8.00 N 1696 7.00 C 6498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.09 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.06 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 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 279 " - pdb=" SG CYS b 292 " distance=2.03 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 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN X 4 " - " MAN X 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-3 " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " " NAG O 1 " - " FUC O 3 " " NAG S 1 " - " FUC S 3 " " NAG V 1 " - " FUC V 3 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG B 301 " - " ASN B 99 " " NAG C 301 " - " ASN C 99 " " NAG D 1 " - " ASN A 119 " " NAG E 1 " - " ASN A 167 " " NAG F 1 " - " ASN A 89 " " NAG G 1 " - " ASN A 224 " " NAG I 1 " - " ASN A 79 " " NAG J 1 " - " ASN A 109 " " NAG K 1 " - " ASN B 79 " " NAG M 1 " - " ASN B 89 " " NAG N 1 " - " ASN B 109 " " NAG O 1 " - " ASN B 119 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN B 224 " " NAG R 1 " - " ASN C 167 " " NAG S 1 " - " ASN C 119 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 89 " " NAG V 1 " - " ASN C 109 " " NAG W 1 " - " ASN C 224 " " NAG X 1 " - " ASN a 365 " " NAG Y 1 " - " ASN a 395 " " NAG Z 1 " - " ASN b 365 " " NAG a 900 " - " ASN a 373 " " NAG a 901 " - " ASN a 390 " " NAG b 701 " - " ASN b 373 " " NAG b 702 " - " ASN b 395 " " NAG b 703 " - " ASN b 390 " " NAG c 701 " - " ASN c 390 " " NAG d 1 " - " ASN c 365 " " NAG e 1 " - " ASN c 373 " " NAG f 1 " - " ASN c 395 " Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 17 sheets defined 41.4% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.897A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.790A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.636A pdb=" N ARG A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'B' and resid 75 through 81 removed outlier: 4.310A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 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 157 through 161 removed outlier: 3.819A pdb=" N LYS B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.925A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 203 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.496A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.688A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.858A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'a' and resid 281 through 285 removed outlier: 4.008A pdb=" N LEU a 285 " --> pdb=" O ARG a 282 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.562A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.594A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 413 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.642A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.546A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 413 Processing helix chain 'c' and resid 281 through 285 removed outlier: 3.546A pdb=" N LEU c 285 " --> pdb=" O ARG c 282 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 334 through 345 removed outlier: 6.003A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.653A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 89 removed outlier: 6.860A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 7 removed outlier: 7.728A pdb=" N UNK H 76 " --> pdb=" O UNK H 72 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N UNK H 72 " --> pdb=" O UNK H 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.868A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N UNK H 96 " --> pdb=" O UNK H 100N" (cutoff:3.500A) removed outlier: 7.650A pdb=" N UNK H 100N" --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N UNK H 98 " --> pdb=" O UNK H 100L" (cutoff:3.500A) removed outlier: 9.357A pdb=" N UNK H 100L" --> pdb=" O UNK H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.868A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.385A pdb=" N UNK L 43 " --> pdb=" O UNK L 39 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N UNK L 39 " --> pdb=" O UNK L 43 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK L 45 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N UNK L 86 " --> pdb=" O UNK L 101 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N UNK L 101 " --> pdb=" O UNK L 86 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N UNK L 88 " --> pdb=" O UNK L 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB4, first strand: chain 'a' and resid 388 through 389 removed outlier: 3.583A pdb=" N SER a 392 " --> pdb=" O SER a 389 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB6, first strand: chain 'b' and resid 388 through 389 removed outlier: 3.584A pdb=" N SER b 392 " --> pdb=" O SER b 389 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB8, first strand: chain 'c' and resid 388 through 389 422 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2176 1.33 - 1.46: 2922 1.46 - 1.58: 5414 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 10644 Sorted by residual: bond pdb=" N ARG b 325 " pdb=" CA ARG b 325 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.28e-02 6.10e+03 8.02e+00 bond pdb=" N THR B 215 " pdb=" CA THR B 215 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.64e+00 bond pdb=" N MET B 214 " pdb=" CA MET B 214 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.21e-02 6.83e+03 7.52e+00 bond pdb=" N CYS A 207 " pdb=" CA CYS A 207 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.33e+00 bond pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.28e+00 ... (remaining 10639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 13579 1.82 - 3.64: 741 3.64 - 5.46: 127 5.46 - 7.28: 16 7.28 - 9.10: 2 Bond angle restraints: 14465 Sorted by residual: angle pdb=" CA CYS C 231 " pdb=" C CYS C 231 " pdb=" O CYS C 231 " ideal model delta sigma weight residual 122.41 117.69 4.72 1.21e+00 6.83e-01 1.52e+01 angle pdb=" CA GLU C 228 " pdb=" C GLU C 228 " pdb=" O GLU C 228 " ideal model delta sigma weight residual 121.45 117.42 4.03 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N PHE C 233 " pdb=" CA PHE C 233 " pdb=" C PHE C 233 " ideal model delta sigma weight residual 113.55 108.96 4.59 1.26e+00 6.30e-01 1.33e+01 angle pdb=" C UNK L 79 " pdb=" N UNK L 80 " pdb=" CA UNK L 80 " ideal model delta sigma weight residual 121.70 128.12 -6.42 1.80e+00 3.09e-01 1.27e+01 angle pdb=" CA THR B 215 " pdb=" C THR B 215 " pdb=" O THR B 215 " ideal model delta sigma weight residual 121.16 117.31 3.85 1.13e+00 7.83e-01 1.16e+01 ... (remaining 14460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 6936 21.64 - 43.27: 257 43.27 - 64.90: 56 64.90 - 86.54: 55 86.54 - 108.17: 32 Dihedral angle restraints: 7336 sinusoidal: 3606 harmonic: 3730 Sorted by residual: dihedral pdb=" CB CYS C 180 " pdb=" SG CYS C 180 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual -86.00 -18.57 -67.43 1 1.00e+01 1.00e-02 5.92e+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 -146.21 60.21 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual -86.00 -30.51 -55.49 1 1.00e+01 1.00e-02 4.16e+01 ... (remaining 7333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1751 0.088 - 0.176: 106 0.176 - 0.264: 18 0.264 - 0.352: 2 0.352 - 0.439: 1 Chirality restraints: 1878 Sorted by residual: chirality pdb=" C1 MAN X 4 " pdb=" O3 BMA X 3 " pdb=" C2 MAN X 4 " pdb=" O5 MAN X 4 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-02 2.50e+03 1.12e+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 -2.22 -0.18 2.00e-02 2.50e+03 8.37e+01 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.00e+01 ... (remaining 1875 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.201 2.00e-02 2.50e+03 1.68e-01 3.52e+02 pdb=" C7 NAG Y 1 " 0.050 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.279 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 703 " 0.119 2.00e-02 2.50e+03 9.88e-02 1.22e+02 pdb=" C7 NAG b 703 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG b 703 " 0.088 2.00e-02 2.50e+03 pdb=" N2 NAG b 703 " -0.160 2.00e-02 2.50e+03 pdb=" O7 NAG b 703 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 901 " -0.108 2.00e-02 2.50e+03 8.90e-02 9.90e+01 pdb=" C7 NAG a 901 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG a 901 " -0.081 2.00e-02 2.50e+03 pdb=" N2 NAG a 901 " 0.143 2.00e-02 2.50e+03 pdb=" O7 NAG a 901 " 0.018 2.00e-02 2.50e+03 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 123 2.66 - 3.22: 9624 3.22 - 3.78: 16023 3.78 - 4.34: 22764 4.34 - 4.90: 36632 Nonbonded interactions: 85166 Sorted by model distance: nonbonded pdb=" OG1 THR A 182 " pdb=" OD1 ASN A 185 " model vdw 2.095 3.040 nonbonded pdb=" O ALA C 195 " pdb=" OG SER C 199 " model vdw 2.103 3.040 nonbonded pdb=" OG SER C 246 " pdb=" OD2 ASP c 347 " model vdw 2.108 3.040 nonbonded pdb=" OG1 THR A 81 " pdb=" OD1 ASN a 319 " model vdw 2.219 3.040 nonbonded pdb=" OG SER b 269 " pdb=" O PRO b 275 " model vdw 2.224 3.040 ... (remaining 85161 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 3) selection = (chain 'd' and resid 1 through 3) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'e' selection = chain 'f' } ncs_group { reference = (chain 'H' and resid 19 through 111) selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) } ncs_group { reference = (chain 'a' and (resid 260 through 413 or resid 900)) selection = (chain 'b' and (resid 260 through 413 or resid 701)) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.290 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.700 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.006 0.052 10644 Z= 0.339 Angle : 0.926 9.102 14465 Z= 0.466 Chirality : 0.050 0.439 1878 Planarity : 0.008 0.168 1748 Dihedral : 15.781 108.175 4853 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1017 helix: -0.30 (0.26), residues: 357 sheet: -0.17 (0.46), residues: 111 loop : -0.38 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 210 HIS 0.008 0.002 HIS C 92 PHE 0.011 0.002 PHE B 117 TYR 0.014 0.001 TYR C 253 ARG 0.004 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: B 185 ASN cc_start: 0.8510 (m-40) cc_final: 0.8283 (m110) REVERT: C 125 LYS cc_start: 0.8535 (tttp) cc_final: 0.8175 (ttpt) REVERT: a 379 ARG cc_start: 0.7321 (ttp-110) cc_final: 0.7033 (mtm110) REVERT: b 270 GLU cc_start: 0.6524 (mm-30) cc_final: 0.4995 (tm-30) REVERT: b 304 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8192 (mmtm) REVERT: b 379 ARG cc_start: 0.8394 (ttm110) cc_final: 0.7321 (tmm160) REVERT: c 300 LYS cc_start: 0.9035 (mttp) cc_final: 0.8805 (mttt) REVERT: c 401 ASP cc_start: 0.8892 (m-30) cc_final: 0.8634 (m-30) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 1.4532 time to fit residues: 300.2345 Evaluate side-chains 159 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.0060 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN C 185 ASN C 218 GLN a 324 GLN b 331 GLN b 354 HIS c 342 ASN c 354 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122490 restraints weight = 11423.635| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.92 r_work: 0.3231 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10644 Z= 0.232 Angle : 0.623 7.336 14465 Z= 0.302 Chirality : 0.043 0.281 1878 Planarity : 0.004 0.038 1748 Dihedral : 10.732 72.232 2894 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.72 % Allowed : 7.63 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.27), residues: 1017 helix: 0.35 (0.28), residues: 345 sheet: 0.17 (0.43), residues: 144 loop : -0.01 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.011 0.001 PHE B 117 TYR 0.013 0.001 TYR C 253 ARG 0.007 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8023 (mp) REVERT: B 134 MET cc_start: 0.9218 (tpp) cc_final: 0.8475 (tpt) REVERT: C 125 LYS cc_start: 0.8630 (tttp) cc_final: 0.8030 (tptp) REVERT: a 282 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7679 (ttp80) REVERT: a 379 ARG cc_start: 0.7035 (ttp-110) cc_final: 0.6741 (mtm110) REVERT: b 270 GLU cc_start: 0.6086 (mm-30) cc_final: 0.4287 (tm-30) REVERT: b 304 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8038 (mmtm) REVERT: b 321 GLN cc_start: 0.8492 (mm110) cc_final: 0.8208 (mm110) REVERT: b 379 ARG cc_start: 0.8285 (ttm110) cc_final: 0.6601 (tmm160) REVERT: b 384 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8283 (mtmt) outliers start: 16 outliers final: 5 residues processed: 184 average time/residue: 1.4415 time to fit residues: 283.3238 Evaluate side-chains 165 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain c residue 295 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 96 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 116 optimal weight: 0.0050 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN C 146 ASN C 218 GLN a 324 GLN b 331 GLN b 354 HIS c 342 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118363 restraints weight = 11511.115| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.92 r_work: 0.3168 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10644 Z= 0.311 Angle : 0.659 10.973 14465 Z= 0.314 Chirality : 0.044 0.286 1878 Planarity : 0.004 0.051 1748 Dihedral : 8.719 69.270 2894 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.47 % Allowed : 8.49 % Favored : 89.03 % 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: 0.09 (0.26), residues: 1017 helix: 0.28 (0.27), residues: 345 sheet: 0.35 (0.42), residues: 147 loop : -0.04 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 283 HIS 0.008 0.002 HIS A 230 PHE 0.013 0.002 PHE B 117 TYR 0.013 0.002 TYR C 253 ARG 0.007 0.001 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8060 (mp) REVERT: C 125 LYS cc_start: 0.8670 (tttp) cc_final: 0.8052 (tptp) REVERT: b 270 GLU cc_start: 0.6210 (mm-30) cc_final: 0.4225 (tm-30) REVERT: b 273 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8210 (p0) REVERT: b 304 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8022 (mmtm) REVERT: b 321 GLN cc_start: 0.8497 (mm110) cc_final: 0.8226 (mm110) REVERT: b 379 ARG cc_start: 0.8311 (ttm110) cc_final: 0.6590 (tmm160) REVERT: b 384 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8347 (mtmt) REVERT: c 270 GLU cc_start: 0.6020 (tp30) cc_final: 0.5329 (mm-30) outliers start: 23 outliers final: 10 residues processed: 173 average time/residue: 1.4961 time to fit residues: 277.4369 Evaluate side-chains 162 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 302 ASN Chi-restraints excluded: chain c residue 332 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN C 218 GLN a 324 GLN b 331 GLN b 354 HIS c 354 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120493 restraints weight = 11360.345| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.92 r_work: 0.3195 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10644 Z= 0.202 Angle : 0.566 7.189 14465 Z= 0.275 Chirality : 0.040 0.251 1878 Planarity : 0.003 0.041 1748 Dihedral : 7.034 63.037 2894 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.69 % Allowed : 9.46 % Favored : 87.85 % 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: 0.25 (0.26), residues: 1017 helix: 0.50 (0.28), residues: 345 sheet: 0.57 (0.43), residues: 147 loop : -0.07 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 PHE 0.008 0.001 PHE A 191 TYR 0.007 0.001 TYR C 253 ARG 0.008 0.000 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7992 (mp) REVERT: A 80 MET cc_start: 0.8517 (mtp) cc_final: 0.8301 (mtt) REVERT: C 82 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7696 (mtm) REVERT: C 95 ILE cc_start: 0.8740 (mt) cc_final: 0.8473 (tt) REVERT: C 125 LYS cc_start: 0.8658 (tttp) cc_final: 0.8056 (tptp) REVERT: a 332 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.6853 (tpt) REVERT: a 379 ARG cc_start: 0.7154 (ttp-110) cc_final: 0.6806 (mtm110) REVERT: b 270 GLU cc_start: 0.5991 (mm-30) cc_final: 0.4098 (tm-30) REVERT: b 273 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8214 (p0) REVERT: b 304 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8039 (mmtm) REVERT: b 321 GLN cc_start: 0.8495 (mm110) cc_final: 0.8229 (mm110) REVERT: b 379 ARG cc_start: 0.8298 (ttm110) cc_final: 0.6621 (tmm160) REVERT: c 270 GLU cc_start: 0.5942 (tp30) cc_final: 0.5230 (mm-30) outliers start: 25 outliers final: 9 residues processed: 172 average time/residue: 1.4507 time to fit residues: 266.9528 Evaluate side-chains 164 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN a 324 GLN b 331 GLN c 342 ASN c 354 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118833 restraints weight = 11336.350| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.94 r_work: 0.3175 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10644 Z= 0.290 Angle : 0.613 7.751 14465 Z= 0.295 Chirality : 0.042 0.263 1878 Planarity : 0.004 0.046 1748 Dihedral : 6.971 63.693 2894 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.47 % Allowed : 11.18 % Favored : 86.34 % 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: 0.18 (0.26), residues: 1017 helix: 0.41 (0.28), residues: 345 sheet: 0.64 (0.42), residues: 132 loop : -0.10 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.010 0.002 PHE B 117 TYR 0.008 0.001 TYR C 129 ARG 0.009 0.000 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8038 (mp) REVERT: A 80 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8320 (mtt) REVERT: C 60 SER cc_start: 0.5941 (t) cc_final: 0.5709 (m) REVERT: C 82 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7724 (mtm) REVERT: C 125 LYS cc_start: 0.8685 (tttp) cc_final: 0.8079 (tptp) REVERT: C 251 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8062 (t0) REVERT: a 332 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.6858 (tpt) REVERT: b 270 GLU cc_start: 0.6099 (mm-30) cc_final: 0.5774 (mm-30) REVERT: b 273 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8224 (p0) REVERT: b 304 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8039 (mmtm) REVERT: b 321 GLN cc_start: 0.8521 (mm110) cc_final: 0.8262 (mm110) REVERT: b 379 ARG cc_start: 0.8352 (ttm110) cc_final: 0.6748 (tmm160) REVERT: b 412 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7876 (p) REVERT: c 270 GLU cc_start: 0.6086 (tp30) cc_final: 0.5466 (mm-30) outliers start: 23 outliers final: 12 residues processed: 167 average time/residue: 1.4309 time to fit residues: 255.1109 Evaluate side-chains 171 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN C 218 GLN a 324 GLN b 331 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119280 restraints weight = 11392.297| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.96 r_work: 0.3174 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10644 Z= 0.247 Angle : 0.584 8.210 14465 Z= 0.282 Chirality : 0.040 0.246 1878 Planarity : 0.004 0.053 1748 Dihedral : 6.476 62.634 2894 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.12 % Allowed : 11.40 % Favored : 85.48 % 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: 0.23 (0.26), residues: 1017 helix: 0.49 (0.28), residues: 345 sheet: 0.71 (0.42), residues: 132 loop : -0.12 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 PHE 0.009 0.002 PHE B 191 TYR 0.015 0.001 TYR B 66 ARG 0.010 0.000 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8040 (mp) REVERT: C 95 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8455 (tt) REVERT: C 125 LYS cc_start: 0.8696 (tttp) cc_final: 0.8077 (tptp) REVERT: a 332 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.6866 (tpt) REVERT: b 273 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8229 (p0) REVERT: b 304 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8102 (mmtm) REVERT: b 321 GLN cc_start: 0.8528 (mm110) cc_final: 0.8254 (mm110) REVERT: b 379 ARG cc_start: 0.8328 (ttm110) cc_final: 0.6787 (tmm160) REVERT: b 384 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8300 (mtmt) REVERT: b 412 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7846 (p) REVERT: c 270 GLU cc_start: 0.6128 (tp30) cc_final: 0.5488 (mm-30) outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 1.3932 time to fit residues: 249.0856 Evaluate side-chains 168 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 116 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 209 ASN B 189 GLN B 218 GLN a 324 GLN b 331 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.140573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116155 restraints weight = 11565.944| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.96 r_work: 0.3164 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10644 Z= 0.409 Angle : 0.688 9.134 14465 Z= 0.327 Chirality : 0.044 0.287 1878 Planarity : 0.004 0.052 1748 Dihedral : 7.107 65.811 2894 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.87 % Allowed : 11.29 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1017 helix: 0.24 (0.28), residues: 345 sheet: 0.70 (0.42), residues: 132 loop : -0.19 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 283 HIS 0.008 0.001 HIS A 230 PHE 0.011 0.002 PHE B 191 TYR 0.017 0.002 TYR B 66 ARG 0.012 0.001 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8168 (mp) REVERT: C 82 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7745 (mtm) REVERT: C 125 LYS cc_start: 0.8726 (tttp) cc_final: 0.8093 (tptp) REVERT: C 251 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.7985 (t0) REVERT: a 332 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.6927 (tpt) REVERT: b 304 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8144 (mmtm) REVERT: b 321 GLN cc_start: 0.8545 (mm110) cc_final: 0.8268 (mm110) REVERT: b 379 ARG cc_start: 0.8354 (ttm110) cc_final: 0.6789 (tmm160) REVERT: b 384 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8385 (mtmt) REVERT: b 412 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7854 (p) REVERT: c 270 GLU cc_start: 0.6210 (tp30) cc_final: 0.5620 (mm-30) outliers start: 36 outliers final: 19 residues processed: 168 average time/residue: 1.3453 time to fit residues: 242.3216 Evaluate side-chains 172 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 302 ASN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 94 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN b 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119345 restraints weight = 11418.969| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.95 r_work: 0.3181 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10644 Z= 0.197 Angle : 0.568 7.811 14465 Z= 0.277 Chirality : 0.039 0.231 1878 Planarity : 0.003 0.058 1748 Dihedral : 6.525 62.212 2894 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.47 % Allowed : 12.90 % Favored : 84.62 % 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: 0.22 (0.26), residues: 1017 helix: 0.53 (0.28), residues: 342 sheet: 0.74 (0.42), residues: 132 loop : -0.15 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.008 0.001 PHE B 191 TYR 0.011 0.001 TYR B 66 ARG 0.013 0.000 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8109 (mp) REVERT: C 125 LYS cc_start: 0.8712 (tttp) cc_final: 0.8080 (tptp) REVERT: C 251 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8122 (t0) REVERT: a 332 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.6859 (tpt) REVERT: b 291 LYS cc_start: 0.8623 (mttm) cc_final: 0.8412 (mttm) REVERT: b 304 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8124 (mmtm) REVERT: b 321 GLN cc_start: 0.8508 (mm110) cc_final: 0.8241 (mm110) REVERT: b 379 ARG cc_start: 0.8332 (ttm110) cc_final: 0.6796 (tmm160) REVERT: b 412 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7860 (p) REVERT: c 270 GLU cc_start: 0.6089 (tp30) cc_final: 0.4920 (mm-30) outliers start: 23 outliers final: 16 residues processed: 169 average time/residue: 1.4363 time to fit residues: 259.8569 Evaluate side-chains 166 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN B 218 GLN B 247 GLN a 324 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.118387 restraints weight = 11483.224| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.94 r_work: 0.3170 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10644 Z= 0.268 Angle : 0.607 11.936 14465 Z= 0.293 Chirality : 0.041 0.245 1878 Planarity : 0.004 0.067 1748 Dihedral : 6.589 62.868 2894 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.12 % Allowed : 12.15 % Favored : 84.73 % 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: 0.20 (0.26), residues: 1017 helix: 0.51 (0.28), residues: 342 sheet: 0.78 (0.42), residues: 132 loop : -0.18 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.009 0.002 PHE b 293 TYR 0.013 0.001 TYR B 66 ARG 0.014 0.000 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 192 MET cc_start: 0.7482 (mtt) cc_final: 0.7256 (tmt) REVERT: C 125 LYS cc_start: 0.8730 (tttp) cc_final: 0.8108 (tptp) REVERT: C 251 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8127 (t0) REVERT: a 332 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.6881 (tpt) REVERT: b 270 GLU cc_start: 0.6051 (mm-30) cc_final: 0.5845 (mm-30) REVERT: b 291 LYS cc_start: 0.8681 (mttm) cc_final: 0.8420 (mttm) REVERT: b 304 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8123 (mmtm) REVERT: b 321 GLN cc_start: 0.8533 (mm110) cc_final: 0.8261 (mm110) REVERT: b 379 ARG cc_start: 0.8347 (ttm110) cc_final: 0.6816 (tmm160) REVERT: b 412 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7918 (p) REVERT: c 270 GLU cc_start: 0.6189 (tp30) cc_final: 0.5532 (mm-30) outliers start: 29 outliers final: 19 residues processed: 162 average time/residue: 1.3941 time to fit residues: 241.5055 Evaluate side-chains 166 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 70 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 99 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN B 218 GLN a 324 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120594 restraints weight = 11363.544| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.93 r_work: 0.3231 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10644 Z= 0.191 Angle : 0.558 9.566 14465 Z= 0.274 Chirality : 0.039 0.219 1878 Planarity : 0.003 0.065 1748 Dihedral : 6.248 62.063 2894 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.47 % Allowed : 12.80 % Favored : 84.73 % 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: 0.31 (0.26), residues: 1017 helix: 0.65 (0.28), residues: 342 sheet: 0.85 (0.42), residues: 132 loop : -0.16 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.007 0.001 PHE B 191 TYR 0.011 0.001 TYR B 66 ARG 0.015 0.000 ARG b 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8098 (mp) REVERT: B 192 MET cc_start: 0.7483 (mtt) cc_final: 0.7277 (tmt) REVERT: C 101 THR cc_start: 0.9156 (m) cc_final: 0.8828 (p) REVERT: C 125 LYS cc_start: 0.8701 (tttp) cc_final: 0.8078 (tptp) REVERT: C 251 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8178 (t0) REVERT: a 332 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.6831 (tpt) REVERT: b 270 GLU cc_start: 0.5978 (mm-30) cc_final: 0.5776 (mm-30) REVERT: b 291 LYS cc_start: 0.8562 (mttm) cc_final: 0.8230 (mttm) REVERT: b 304 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8086 (mmtm) REVERT: b 321 GLN cc_start: 0.8504 (mm110) cc_final: 0.8242 (mm110) REVERT: b 379 ARG cc_start: 0.8330 (ttm110) cc_final: 0.6812 (tmm160) REVERT: b 412 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7939 (p) REVERT: c 270 GLU cc_start: 0.6049 (tp30) cc_final: 0.5408 (mm-30) outliers start: 23 outliers final: 17 residues processed: 164 average time/residue: 1.4377 time to fit residues: 251.8665 Evaluate side-chains 171 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 86 optimal weight: 0.0170 chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN a 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121900 restraints weight = 11293.350| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.92 r_work: 0.3247 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 10644 Z= 0.174 Angle : 0.562 13.545 14465 Z= 0.277 Chirality : 0.039 0.318 1878 Planarity : 0.003 0.065 1748 Dihedral : 5.932 61.929 2894 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.58 % Allowed : 12.58 % Favored : 84.84 % 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: 0.39 (0.27), residues: 1017 helix: 0.75 (0.29), residues: 342 sheet: 0.97 (0.43), residues: 132 loop : -0.16 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 283 HIS 0.005 0.001 HIS A 230 PHE 0.008 0.001 PHE b 293 TYR 0.010 0.001 TYR B 66 ARG 0.016 0.000 ARG b 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7643.42 seconds wall clock time: 137 minutes 43.36 seconds (8263.36 seconds total)