Starting phenix.real_space_refine on Fri Oct 11 20:34:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyc_41713/10_2024/8tyc_41713.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyc_41713/10_2024/8tyc_41713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyc_41713/10_2024/8tyc_41713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyc_41713/10_2024/8tyc_41713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyc_41713/10_2024/8tyc_41713.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyc_41713/10_2024/8tyc_41713.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 6603 2.51 5 N 1712 2.21 5 O 2220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 10628 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1536 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1583 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 195} Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1548 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "a" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1256 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain breaks: 1 Chain: "b" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1269 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "c" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1306 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 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: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" 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: "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: 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: "W" 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: "X" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 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: "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: "h" 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: "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: "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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.91, per 1000 atoms: 0.74 Number of scatterers: 10628 At special positions: 0 Unit cell: (111.622, 109.956, 109.123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 2220 8.00 N 1712 7.00 C 6603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, 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=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.02 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.01 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.04 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.01 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.04 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.01 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 Z 4 " - " MAN Z 5 " " MAN f 4 " - " MAN f 5 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA Z 3 " - " MAN Z 4 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 6 " " BMA f 3 " - " MAN f 6 " " BMA h 3 " - " MAN h 6 " BETA1-3 " NAG Q 1 " - " FUC Q 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " 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 e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " BETA1-6 " NAG W 1 " - " FUC W 3 " NAG-ASN " NAG C 301 " - " ASN C 99 " " NAG D 1 " - " ASN A 119 " " NAG E 1 " - " ASN A 79 " " NAG F 1 " - " ASN A 89 " " NAG G 1 " - " ASN A 99 " " NAG I 1 " - " ASN A 109 " " NAG J 1 " - " ASN A 167 " " NAG K 1 " - " ASN A 224 " " NAG M 1 " - " ASN B 99 " " NAG N 1 " - " ASN B 224 " " NAG O 1 " - " ASN B 167 " " NAG P 1 " - " ASN B 119 " " NAG Q 1 " - " ASN B 109 " " NAG R 1 " - " ASN B 89 " " NAG S 1 " - " ASN B 79 " " NAG T 1 " - " ASN C 119 " " NAG U 1 " - " ASN C 79 " " NAG V 1 " - " ASN C 89 " " NAG W 1 " - " ASN C 109 " " NAG X 1 " - " ASN C 167 " " NAG Y 1 " - " ASN C 224 " " NAG Z 1 " - " ASN a 365 " " NAG a 701 " - " ASN a 395 " " NAG a 702 " - " ASN a 390 " " NAG b 701 " - " ASN b 390 " " NAG c 701 " - " ASN c 395 " " NAG c 702 " - " ASN c 390 " " NAG d 1 " - " ASN a 373 " " NAG e 1 " - " ASN b 373 " " NAG f 1 " - " ASN b 365 " " NAG g 1 " - " ASN b 395 " " NAG h 1 " - " ASN c 365 " " NAG i 1 " - " ASN c 373 " Time building additional restraints: 4.21 Conformation dependent library (CDL) restraints added in 1.3 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 15 sheets defined 43.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.637A 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 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.946A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 142 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 Processing helix chain 'B' and resid 183 through 195 removed outlier: 4.124A pdb=" N GLN B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.194A pdb=" N MET C 80 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 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 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.637A pdb=" N ARG C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.948A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.562A pdb=" N UNK H 32 " --> pdb=" O UNK H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'a' and resid 281 through 285 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: 5.528A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU a 344 " --> pdb=" O ALA a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 420 Processing helix chain 'b' and resid 281 through 285 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: 4.968A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 347 through 359 Processing helix chain 'b' and resid 399 through 420 Processing helix chain 'c' and resid 281 through 285 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 removed outlier: 3.559A pdb=" N GLN c 324 " --> pdb=" O LYS c 320 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.599A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.500A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 396 through 398 No H-bonds generated for 'chain 'c' and resid 396 through 398' Processing helix chain 'c' and resid 399 through 420 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 removed outlier: 3.600A pdb=" N GLY A 102 " --> pdb=" O THR A 225 " (cutoff:3.500A) 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 84 through 87 removed outlier: 3.541A pdb=" N GLY C 102 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.012A pdb=" N UNK H 45 " --> pdb=" O UNK H 39 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N UNK H 39 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N UNK H 47 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N UNK H 37 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N UNK H 49 " --> pdb=" O UNK H 35 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N UNK H 35 " --> pdb=" O UNK H 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 52 through 53 removed outlier: 4.346A pdb=" N UNK L 44 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N UNK L 37 " --> pdb=" O UNK L 44 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N UNK L 46 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N UNK L 35 " --> pdb=" O UNK L 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB5, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB6, first strand: chain 'c' and resid 388 through 389 425 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2494 1.33 - 1.47: 3481 1.47 - 1.61: 4690 1.61 - 1.75: 8 1.75 - 1.89: 139 Bond restraints: 10812 Sorted by residual: bond pdb=" CA SER C 121 " pdb=" CB SER C 121 " ideal model delta sigma weight residual 1.527 1.427 0.100 1.15e-02 7.56e+03 7.55e+01 bond pdb=" CB LEU B 259 " pdb=" CG LEU B 259 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" CB HIS A 115 " pdb=" CG HIS A 115 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.66e+01 bond pdb=" NE1 TRP b 386 " pdb=" CE2 TRP b 386 " ideal model delta sigma weight residual 1.370 1.309 0.061 1.10e-02 8.26e+03 3.10e+01 bond pdb=" CB LEU A 259 " pdb=" CG LEU A 259 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.96e+01 ... (remaining 10807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 13517 3.09 - 6.18: 1087 6.18 - 9.27: 68 9.27 - 12.36: 5 12.36 - 15.44: 2 Bond angle restraints: 14679 Sorted by residual: angle pdb=" N ILE b 350 " pdb=" CA ILE b 350 " pdb=" C ILE b 350 " ideal model delta sigma weight residual 111.58 101.80 9.78 1.06e+00 8.90e-01 8.51e+01 angle pdb=" N SER c 269 " pdb=" CA SER c 269 " pdb=" C SER c 269 " ideal model delta sigma weight residual 111.07 119.14 -8.07 1.07e+00 8.73e-01 5.69e+01 angle pdb=" C ALA c 328 " pdb=" N PRO c 329 " pdb=" CA PRO c 329 " ideal model delta sigma weight residual 120.31 127.42 -7.11 9.80e-01 1.04e+00 5.26e+01 angle pdb=" N LEU c 349 " pdb=" CA LEU c 349 " pdb=" C LEU c 349 " ideal model delta sigma weight residual 111.69 103.48 8.21 1.23e+00 6.61e-01 4.45e+01 angle pdb=" CA ASP a 357 " pdb=" CB ASP a 357 " pdb=" CG ASP a 357 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.37e+01 ... (remaining 14674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 7118 21.41 - 42.83: 207 42.83 - 64.24: 48 64.24 - 85.66: 72 85.66 - 107.07: 42 Dihedral angle restraints: 7487 sinusoidal: 3742 harmonic: 3745 Sorted by residual: 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 -141.13 55.13 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" CA CYS B 118 " pdb=" CB CYS B 118 " pdb=" SG CYS B 118 " pdb=" SG CYS B 155 " ideal model delta sinusoidal sigma weight residual 79.00 7.75 71.25 1 2.00e+01 2.50e-03 1.63e+01 dihedral pdb=" O4 BMA h 3 " pdb=" C4 BMA h 3 " pdb=" C5 BMA h 3 " pdb=" O5 BMA h 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.36 107.07 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 7484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1531 0.183 - 0.366: 289 0.366 - 0.549: 81 0.549 - 0.732: 1 0.732 - 0.915: 1 Chirality restraints: 1903 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.14e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.77e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.75e+02 ... (remaining 1900 not shown) Planarity restraints: 1795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.11e+03 pdb=" C7 NAG T 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.127 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 1 " -0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG g 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG g 1 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG g 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG g 1 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 2 " -0.312 2.00e-02 2.50e+03 2.63e-01 8.66e+02 pdb=" C7 NAG g 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG g 2 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG g 2 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG g 2 " -0.037 2.00e-02 2.50e+03 ... (remaining 1792 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3855 2.87 - 3.38: 10103 3.38 - 3.89: 17579 3.89 - 4.39: 21043 4.39 - 4.90: 32250 Nonbonded interactions: 84830 Sorted by model distance: nonbonded pdb=" O ALA A 195 " pdb=" O GLY A 197 " model vdw 2.365 3.040 nonbonded pdb=" N ASP C 122 " pdb=" N ALA C 123 " model vdw 2.367 2.560 nonbonded pdb=" OD2 ASP B 251 " pdb=" NZ LYS c 339 " model vdw 2.369 3.120 nonbonded pdb=" O SER C 121 " pdb=" OG SER C 121 " model vdw 2.376 3.040 nonbonded pdb=" N ASP B 251 " pdb=" OD1 ASP B 251 " model vdw 2.388 3.120 ... (remaining 84825 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' and (resid 60 through 171 or resid 179 through 259)) selection = (chain 'C' and (resid 60 through 171 or resid 179 through 259)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) } ncs_group { reference = (chain 'H' and resid 4 through 111) selection = chain 'L' } ncs_group { reference = chain 'Z' selection = chain 'f' selection = chain 'h' } ncs_group { reference = (chain 'a' and (resid 260 through 420 or resid 701)) selection = (chain 'b' and (resid 260 through 268 or resid 276 through 420 or resid 701)) selection = (chain 'c' and (resid 260 through 268 or resid 276 through 420 or resid 701)) } 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: 0.010 Normalize map: mean=0, sd=1: 2.090 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: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 29.240 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.021 0.133 10812 Z= 1.308 Angle : 1.753 15.444 14679 Z= 1.067 Chirality : 0.154 0.915 1903 Planarity : 0.016 0.297 1762 Dihedral : 16.239 107.073 4999 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 0.44 (0.25), residues: 1038 helix: -0.37 (0.25), residues: 365 sheet: 1.14 (0.48), residues: 111 loop : 0.79 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.010 TRP C 196 HIS 0.012 0.003 HIS a 354 PHE 0.025 0.004 PHE A 233 TYR 0.063 0.009 TYR C 253 ARG 0.006 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 405 GLN cc_start: 0.8519 (tp40) cc_final: 0.7979 (tp-100) REVERT: a 409 ASN cc_start: 0.8895 (m-40) cc_final: 0.8623 (m-40) REVERT: c 406 GLN cc_start: 0.8649 (tp40) cc_final: 0.8215 (tp-100) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2872 time to fit residues: 122.1748 Evaluate side-chains 179 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 92 HIS B 165 GLN C 149 GLN C 179 HIS b 348 GLN b 409 ASN c 348 GLN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10812 Z= 0.260 Angle : 0.848 11.608 14679 Z= 0.420 Chirality : 0.050 0.587 1903 Planarity : 0.004 0.040 1762 Dihedral : 13.136 85.034 2987 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.05 % Allowed : 10.20 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.12 (0.25), residues: 1038 helix: 0.91 (0.28), residues: 354 sheet: 2.36 (0.50), residues: 93 loop : 0.51 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 210 HIS 0.007 0.002 HIS A 141 PHE 0.018 0.002 PHE c 293 TYR 0.019 0.002 TYR A 94 ARG 0.004 0.001 ARG c 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 85 SER cc_start: 0.7141 (OUTLIER) cc_final: 0.6833 (p) REVERT: a 405 GLN cc_start: 0.8484 (tp40) cc_final: 0.7246 (tp-100) REVERT: a 409 ASN cc_start: 0.8778 (m-40) cc_final: 0.8574 (m-40) REVERT: b 406 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7867 (mm-40) REVERT: c 406 GLN cc_start: 0.8737 (tp40) cc_final: 0.8302 (tp-100) REVERT: c 410 MET cc_start: 0.7008 (mmm) cc_final: 0.6780 (mmm) outliers start: 29 outliers final: 12 residues processed: 225 average time/residue: 0.2380 time to fit residues: 74.5919 Evaluate side-chains 190 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 177 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 0.0870 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN c 354 HIS c 374 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10812 Z= 0.217 Angle : 0.768 20.610 14679 Z= 0.378 Chirality : 0.048 0.533 1903 Planarity : 0.003 0.044 1762 Dihedral : 9.686 76.801 2987 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.05 % Allowed : 12.09 % Favored : 84.86 % 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: 0.90 (0.26), residues: 1038 helix: 1.08 (0.28), residues: 362 sheet: 1.81 (0.48), residues: 116 loop : 0.09 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 210 HIS 0.006 0.001 HIS C 230 PHE 0.013 0.001 PHE a 399 TYR 0.022 0.002 TYR c 366 ARG 0.003 0.001 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 214 MET cc_start: 0.8541 (mtm) cc_final: 0.8315 (mtt) REVERT: a 406 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8823 (tp-100) REVERT: a 408 ASP cc_start: 0.8617 (p0) cc_final: 0.8390 (p0) REVERT: b 283 TRP cc_start: 0.7506 (m100) cc_final: 0.7280 (m100) REVERT: b 327 LYS cc_start: 0.8146 (ptmt) cc_final: 0.7937 (pttt) REVERT: b 401 ASP cc_start: 0.8516 (t70) cc_final: 0.8165 (t0) REVERT: b 406 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7576 (mm-40) REVERT: c 406 GLN cc_start: 0.8745 (tp40) cc_final: 0.8403 (tp-100) outliers start: 29 outliers final: 13 residues processed: 210 average time/residue: 0.2437 time to fit residues: 72.2967 Evaluate side-chains 196 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 chunk 58 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 59 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS C 146 ASN ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 348 GLN c 354 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10812 Z= 0.193 Angle : 0.741 25.516 14679 Z= 0.363 Chirality : 0.047 0.510 1903 Planarity : 0.003 0.044 1762 Dihedral : 8.334 69.111 2987 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.10 % Allowed : 14.51 % Favored : 83.39 % 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: 0.91 (0.26), residues: 1038 helix: 1.23 (0.28), residues: 362 sheet: 1.51 (0.47), residues: 127 loop : 0.03 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 210 HIS 0.004 0.001 HIS C 141 PHE 0.015 0.001 PHE C 233 TYR 0.030 0.001 TYR c 366 ARG 0.005 0.000 ARG c 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 339 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8186 (pttm) REVERT: b 283 TRP cc_start: 0.7435 (m100) cc_final: 0.7219 (m100) REVERT: c 405 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8587 (tm-30) REVERT: c 406 GLN cc_start: 0.8729 (tp40) cc_final: 0.8330 (tp-100) outliers start: 20 outliers final: 11 residues processed: 210 average time/residue: 0.2245 time to fit residues: 66.7015 Evaluate side-chains 196 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 305 HIS b 405 GLN c 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10812 Z= 0.237 Angle : 0.780 23.294 14679 Z= 0.380 Chirality : 0.048 0.519 1903 Planarity : 0.003 0.043 1762 Dihedral : 7.941 63.190 2987 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.26 % Allowed : 14.30 % Favored : 82.44 % 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: 0.61 (0.26), residues: 1038 helix: 1.01 (0.28), residues: 367 sheet: 1.40 (0.45), residues: 125 loop : -0.19 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 210 HIS 0.006 0.001 HIS C 141 PHE 0.009 0.001 PHE b 399 TYR 0.034 0.002 TYR c 366 ARG 0.011 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 MET cc_start: 0.8193 (tmm) cc_final: 0.7975 (tmm) REVERT: a 339 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8201 (pttm) REVERT: a 410 MET cc_start: 0.7209 (mmm) cc_final: 0.6984 (mtp) REVERT: b 283 TRP cc_start: 0.7440 (m100) cc_final: 0.7213 (m100) outliers start: 31 outliers final: 21 residues processed: 211 average time/residue: 0.1839 time to fit residues: 55.8118 Evaluate side-chains 205 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 339 LYS Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain c residue 401 ASP Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 29 optimal weight: 0.2980 chunk 119 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 30.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN ** b 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 302 ASN ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10812 Z= 0.257 Angle : 0.788 20.499 14679 Z= 0.384 Chirality : 0.050 0.557 1903 Planarity : 0.003 0.052 1762 Dihedral : 7.748 59.796 2987 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.47 % Allowed : 15.25 % Favored : 81.28 % 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: 0.70 (0.26), residues: 1038 helix: 1.17 (0.28), residues: 363 sheet: 1.47 (0.46), residues: 115 loop : -0.17 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 210 HIS 0.006 0.001 HIS C 141 PHE 0.012 0.001 PHE a 262 TYR 0.023 0.001 TYR c 366 ARG 0.011 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.7311 (mmm) cc_final: 0.7047 (tpp) REVERT: b 283 TRP cc_start: 0.7450 (m100) cc_final: 0.7226 (m100) REVERT: b 414 MET cc_start: 0.7356 (mmm) cc_final: 0.7112 (mmm) REVERT: c 405 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8705 (tm-30) outliers start: 33 outliers final: 23 residues processed: 209 average time/residue: 0.2286 time to fit residues: 68.3916 Evaluate side-chains 194 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN c 302 ASN ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 374 HIS c 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10812 Z= 0.372 Angle : 0.867 19.232 14679 Z= 0.419 Chirality : 0.052 0.543 1903 Planarity : 0.004 0.047 1762 Dihedral : 7.984 57.122 2987 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.00 % Allowed : 14.51 % Favored : 81.49 % 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: 0.45 (0.26), residues: 1038 helix: 0.92 (0.28), residues: 364 sheet: 1.23 (0.44), residues: 129 loop : -0.30 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 210 HIS 0.013 0.002 HIS A 93 PHE 0.013 0.002 PHE a 262 TYR 0.025 0.002 TYR c 366 ARG 0.009 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8670 (tp30) cc_final: 0.8282 (tm-30) REVERT: a 406 GLN cc_start: 0.9146 (tp40) cc_final: 0.8928 (tp-100) REVERT: a 410 MET cc_start: 0.7523 (mmm) cc_final: 0.7298 (mtp) REVERT: b 283 TRP cc_start: 0.7491 (m100) cc_final: 0.7245 (m100) REVERT: b 413 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7761 (tm-30) REVERT: c 405 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8753 (tm-30) REVERT: c 410 MET cc_start: 0.6553 (mmm) cc_final: 0.6339 (mmm) outliers start: 38 outliers final: 23 residues processed: 208 average time/residue: 0.1565 time to fit residues: 46.8457 Evaluate side-chains 193 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 300 LYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 36 optimal weight: 0.0170 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 81 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN a 405 GLN ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 374 HIS c 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10812 Z= 0.359 Angle : 0.870 19.673 14679 Z= 0.420 Chirality : 0.052 0.534 1903 Planarity : 0.004 0.055 1762 Dihedral : 7.965 54.522 2987 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.15 % Allowed : 16.19 % Favored : 80.65 % 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: 0.39 (0.26), residues: 1038 helix: 0.89 (0.28), residues: 364 sheet: 1.19 (0.45), residues: 127 loop : -0.36 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 210 HIS 0.010 0.001 HIS A 93 PHE 0.013 0.002 PHE a 316 TYR 0.026 0.002 TYR a 366 ARG 0.012 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8654 (tp30) cc_final: 0.8350 (tm-30) REVERT: B 175 ASP cc_start: 0.6070 (p0) cc_final: 0.5768 (p0) REVERT: B 192 MET cc_start: 0.8423 (tmm) cc_final: 0.8152 (tmm) REVERT: b 283 TRP cc_start: 0.7482 (m100) cc_final: 0.7246 (m100) REVERT: b 413 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7737 (tm-30) REVERT: c 300 LYS cc_start: 0.8995 (mttp) cc_final: 0.8733 (mptt) REVERT: c 396 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7885 (tm-30) REVERT: c 405 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8539 (tm-30) outliers start: 30 outliers final: 24 residues processed: 197 average time/residue: 0.2343 time to fit residues: 64.8364 Evaluate side-chains 190 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 300 LYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: