Starting phenix.real_space_refine on Fri Oct 11 18:45:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcv_43141/10_2024/8vcv_43141.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcv_43141/10_2024/8vcv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcv_43141/10_2024/8vcv_43141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcv_43141/10_2024/8vcv_43141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcv_43141/10_2024/8vcv_43141.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcv_43141/10_2024/8vcv_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-5477/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: 9.66, per 1000 atoms: 0.92 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: 3.61 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: 1.32 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: 3.43 Time building geometry restraints manager: 4.04 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: 7.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.720 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.530 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.252 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: 1.4611 time to fit residues: 302.0829 Evaluate side-chains 159 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7803 (mp) REVERT: B 134 MET cc_start: 0.9137 (tpp) cc_final: 0.8310 (tpt) REVERT: C 125 LYS cc_start: 0.8548 (tttp) cc_final: 0.8147 (tptp) REVERT: b 270 GLU cc_start: 0.6316 (mm-30) cc_final: 0.4738 (tm-30) REVERT: b 304 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8252 (mmtm) REVERT: b 379 ARG cc_start: 0.8540 (ttm110) cc_final: 0.7402 (tmm160) REVERT: b 384 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8484 (mtmt) outliers start: 16 outliers final: 5 residues processed: 184 average time/residue: 1.4387 time to fit residues: 282.0705 Evaluate side-chains 164 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 63 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10644 Z= 0.370 Angle : 0.721 13.415 14465 Z= 0.340 Chirality : 0.046 0.306 1878 Planarity : 0.005 0.063 1748 Dihedral : 8.917 70.444 2894 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.90 % Allowed : 8.39 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1017 helix: 0.12 (0.27), residues: 345 sheet: 0.30 (0.42), residues: 147 loop : -0.10 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP c 283 HIS 0.009 0.002 HIS c 398 PHE 0.016 0.002 PHE B 117 TYR 0.016 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 fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7922 (mp) REVERT: B 134 MET cc_start: 0.9110 (tpp) cc_final: 0.8402 (tpt) REVERT: C 125 LYS cc_start: 0.8628 (tttp) cc_final: 0.8205 (tptp) REVERT: b 273 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7962 (p0) REVERT: b 304 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8341 (mmtm) REVERT: b 379 ARG cc_start: 0.8573 (ttm110) cc_final: 0.7394 (tmm160) REVERT: b 384 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8584 (mtmt) REVERT: c 270 GLU cc_start: 0.6157 (tp30) cc_final: 0.5597 (mm-30) outliers start: 27 outliers final: 12 residues processed: 173 average time/residue: 1.4598 time to fit residues: 269.2637 Evaluate side-chains 163 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 367 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 112 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 C 218 GLN a 324 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 354 HIS c 354 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10644 Z= 0.298 Angle : 0.630 7.116 14465 Z= 0.303 Chirality : 0.043 0.275 1878 Planarity : 0.004 0.044 1748 Dihedral : 7.540 66.152 2894 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.55 % Allowed : 9.14 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1017 helix: 0.25 (0.27), residues: 345 sheet: 0.51 (0.41), residues: 132 loop : -0.12 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 PHE 0.010 0.002 PHE B 233 TYR 0.009 0.001 TYR C 253 ARG 0.007 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 189 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7870 (mp) REVERT: C 82 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7810 (mtm) REVERT: C 125 LYS cc_start: 0.8636 (tttp) cc_final: 0.8210 (tptp) REVERT: C 251 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7997 (t0) REVERT: a 332 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.6601 (tpt) REVERT: b 270 GLU cc_start: 0.6353 (mm-30) cc_final: 0.6147 (mm-30) REVERT: b 304 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8333 (mmtm) REVERT: b 379 ARG cc_start: 0.8606 (ttm110) cc_final: 0.7460 (tmm160) REVERT: c 270 GLU cc_start: 0.6069 (tp30) cc_final: 0.5480 (mm-30) outliers start: 33 outliers final: 12 residues processed: 168 average time/residue: 1.4996 time to fit residues: 269.0456 Evaluate side-chains 164 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain B residue 231 CYS 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 332 MET Chi-restraints excluded: chain a residue 333 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 c residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 0.2980 chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 331 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10644 Z= 0.214 Angle : 0.574 7.894 14465 Z= 0.278 Chirality : 0.040 0.244 1878 Planarity : 0.004 0.048 1748 Dihedral : 6.714 62.263 2894 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.47 % Allowed : 11.40 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1017 helix: 0.43 (0.28), residues: 345 sheet: 0.65 (0.42), residues: 132 loop : -0.10 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 PHE 0.008 0.002 PHE A 191 TYR 0.012 0.001 TYR B 66 ARG 0.008 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 187 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 125 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8157 (tptt) REVERT: C 125 LYS cc_start: 0.8628 (tttp) cc_final: 0.8213 (tptp) REVERT: a 332 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.6568 (tpt) REVERT: b 304 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8271 (mmtm) REVERT: b 379 ARG cc_start: 0.8588 (ttm110) cc_final: 0.7543 (tmm160) REVERT: c 270 GLU cc_start: 0.6042 (tp30) cc_final: 0.5460 (mm-30) outliers start: 23 outliers final: 15 residues processed: 174 average time/residue: 1.4414 time to fit residues: 267.6743 Evaluate side-chains 163 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 125 LYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 180 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 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 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 302 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 10.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 331 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10644 Z= 0.213 Angle : 0.566 9.037 14465 Z= 0.275 Chirality : 0.040 0.238 1878 Planarity : 0.003 0.048 1748 Dihedral : 6.371 62.691 2894 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.90 % Allowed : 11.61 % 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: 0.28 (0.26), residues: 1017 helix: 0.54 (0.28), residues: 345 sheet: 0.76 (0.42), residues: 132 loop : -0.09 (0.28), residues: 540 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 0.010 0.001 PHE B 191 TYR 0.011 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 182 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7813 (mp) REVERT: C 125 LYS cc_start: 0.8643 (tttp) cc_final: 0.8223 (tptp) REVERT: C 251 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8076 (t0) REVERT: a 332 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.6595 (tpt) REVERT: b 304 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8266 (mmtm) REVERT: b 379 ARG cc_start: 0.8577 (ttm110) cc_final: 0.7542 (tmm160) REVERT: c 270 GLU cc_start: 0.6053 (tp30) cc_final: 0.5704 (mm-30) outliers start: 27 outliers final: 16 residues processed: 168 average time/residue: 1.3524 time to fit residues: 243.3878 Evaluate side-chains 165 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 95 ILE Chi-restraints excluded: chain B residue 180 CYS 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 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 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 341 VAL 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 13 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 189 GLN A 209 ASN A 218 GLN B 189 GLN B 218 GLN a 324 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 331 GLN c 354 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10644 Z= 0.447 Angle : 0.725 8.962 14465 Z= 0.343 Chirality : 0.046 0.304 1878 Planarity : 0.004 0.056 1748 Dihedral : 7.422 67.108 2894 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.66 % Allowed : 11.72 % 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: -0.03 (0.26), residues: 1017 helix: 0.17 (0.27), residues: 345 sheet: 0.66 (0.42), residues: 132 loop : -0.22 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 283 HIS 0.009 0.001 HIS A 230 PHE 0.012 0.002 PHE B 233 TYR 0.018 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 181 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8021 (mp) REVERT: C 82 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7840 (mtm) REVERT: C 125 LYS cc_start: 0.8688 (tttp) cc_final: 0.8241 (tptp) REVERT: C 251 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7873 (t0) REVERT: a 332 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.6715 (tpt) REVERT: b 304 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8374 (mmtm) REVERT: b 379 ARG cc_start: 0.8589 (ttm110) cc_final: 0.7520 (tmm160) REVERT: b 384 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8555 (mtmt) REVERT: c 270 GLU cc_start: 0.6229 (tp30) cc_final: 0.5907 (mm-30) outliers start: 34 outliers final: 21 residues processed: 163 average time/residue: 1.3795 time to fit residues: 240.9278 Evaluate side-chains 165 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 95 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 82 MET 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 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 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 334 ILE Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 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 71 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN a 324 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 331 GLN c 354 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10644 Z= 0.243 Angle : 0.595 10.428 14465 Z= 0.287 Chirality : 0.041 0.242 1878 Planarity : 0.004 0.057 1748 Dihedral : 6.779 62.773 2894 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.69 % Allowed : 12.90 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1017 helix: 0.45 (0.28), residues: 342 sheet: 0.75 (0.42), residues: 132 loop : -0.24 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 PHE 0.008 0.001 PHE c 399 TYR 0.014 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 176 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7970 (mp) REVERT: C 125 LYS cc_start: 0.8678 (tttp) cc_final: 0.8229 (tptp) REVERT: C 251 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8001 (t0) REVERT: a 332 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.6630 (tpt) REVERT: b 304 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8330 (mmtm) REVERT: b 379 ARG cc_start: 0.8582 (ttm110) cc_final: 0.7535 (tmm160) REVERT: c 270 GLU cc_start: 0.6060 (tp30) cc_final: 0.5679 (mm-30) outliers start: 25 outliers final: 18 residues processed: 164 average time/residue: 1.3712 time to fit residues: 241.2806 Evaluate side-chains 166 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 180 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 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 334 ILE Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain c residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 331 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2448 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= 0.185 Angle : 0.548 9.721 14465 Z= 0.268 Chirality : 0.039 0.219 1878 Planarity : 0.003 0.058 1748 Dihedral : 6.215 62.551 2894 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.58 % Allowed : 13.23 % Favored : 84.19 % 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: 0.30 (0.26), residues: 1017 helix: 0.65 (0.28), residues: 342 sheet: 0.88 (0.43), residues: 132 loop : -0.19 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.005 0.001 HIS A 230 PHE 0.008 0.001 PHE c 399 TYR 0.011 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 fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 192 MET cc_start: 0.7702 (tmt) cc_final: 0.7426 (mtt) REVERT: C 125 LYS cc_start: 0.8671 (tttp) cc_final: 0.8236 (tptp) REVERT: C 251 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8068 (t0) REVERT: a 332 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.6564 (tpt) REVERT: b 304 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8307 (mmtm) REVERT: b 379 ARG cc_start: 0.8574 (ttm110) cc_final: 0.7546 (tmm160) REVERT: c 270 GLU cc_start: 0.6032 (tp30) cc_final: 0.5676 (mm-30) outliers start: 24 outliers final: 16 residues processed: 164 average time/residue: 1.3962 time to fit residues: 245.1902 Evaluate side-chains 162 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 180 CYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain C residue 95 ILE 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 c residue 290 LEU 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 72 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 0.0470 chunk 99 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.8284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 218 GLN B 189 GLN B 218 GLN B 247 GLN a 324 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10644 Z= 0.385 Angle : 0.677 11.901 14465 Z= 0.323 Chirality : 0.044 0.275 1878 Planarity : 0.004 0.069 1748 Dihedral : 6.875 64.397 2894 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.80 % Allowed : 12.90 % Favored : 84.30 % 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: 0.36 (0.28), residues: 342 sheet: 0.81 (0.42), residues: 132 loop : -0.23 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 283 HIS 0.007 0.001 HIS A 230 PHE 0.011 0.002 PHE b 293 TYR 0.017 0.002 TYR B 66 ARG 0.015 0.001 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 170 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 125 LYS cc_start: 0.8704 (tttp) cc_final: 0.8249 (tptp) REVERT: C 251 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8052 (t0) REVERT: a 332 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.6687 (tpt) REVERT: b 304 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8347 (mmtm) REVERT: b 379 ARG cc_start: 0.8588 (ttm110) cc_final: 0.7535 (tmm160) REVERT: c 270 GLU cc_start: 0.6138 (tp30) cc_final: 0.5572 (mm-30) outliers start: 26 outliers final: 20 residues processed: 158 average time/residue: 1.4185 time to fit residues: 240.0222 Evaluate side-chains 164 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 95 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain C residue 95 ILE 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 334 ILE Chi-restraints excluded: chain b residue 341 VAL 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 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.0050 chunk 5 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120051 restraints weight = 11302.761| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.93 r_work: 0.3224 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2531 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= 0.180 Angle : 0.556 9.579 14465 Z= 0.272 Chirality : 0.039 0.214 1878 Planarity : 0.003 0.062 1748 Dihedral : 6.182 61.940 2894 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.04 % Allowed : 13.66 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1017 helix: 0.35 (0.28), residues: 360 sheet: 0.89 (0.43), residues: 132 loop : -0.23 (0.28), residues: 525 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 309 TYR 0.012 0.001 TYR B 66 ARG 0.015 0.000 ARG b 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4663.43 seconds wall clock time: 84 minutes 38.84 seconds (5078.84 seconds total)