Starting phenix.real_space_refine (version: dev) on Sat Feb 25 16:21:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2023/7wm4_32599.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2023/7wm4_32599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2023/7wm4_32599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2023/7wm4_32599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2023/7wm4_32599.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2023/7wm4_32599.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.017 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 Process input model Symmetric amino acids flipped Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 497": "OD1" <-> "OD2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 25848 Number of models: 1 Model: "" Number of chains: 38 Chain: "C" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5310 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 632} Chain breaks: 2 Chain: "D" Number of atoms: 5360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5360 Classifications: {'peptide': 668} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 639} Chain breaks: 1 Chain: "E" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5310 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 632} Chain breaks: 2 Chain: "F" Number of atoms: 5360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5360 Classifications: {'peptide': 668} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 639} Chain breaks: 1 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1702 Classifications: {'RNA': 81} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 39, 'rna3p_pyr': 39} Link IDs: {'rna2p': 3, 'rna3p': 77} Chain: "B" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1700 Classifications: {'RNA': 81} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 39, 'rna3p_pyr': 41} Link IDs: {'rna2p': 1, 'rna3p': 79} Chain: "G" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "K" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: 1 Unresolved non-hydrogen chiralities: 3 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "Q" 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: 1 Unresolved non-hydrogen chiralities: 3 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: 1 Unresolved non-hydrogen chiralities: 3 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: 1 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 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: 1 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 chiralities: 2 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 chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "Z" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "a" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "f" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "g" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 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 chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 14.33, per 1000 atoms: 0.55 Number of scatterers: 25848 At special positions: 0 Unit cell: (223.344, 181.608, 110.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 162 15.00 O 5562 8.00 N 4273 7.00 C 15795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS C 29 " - pdb=" SG CYS C 38 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 650 " - pdb=" SG CYS C 678 " distance=2.03 Simple disulfide: pdb=" SG CYS C 652 " - pdb=" SG CYS C 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 38 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 650 " - pdb=" SG CYS D 678 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 38 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 650 " - pdb=" SG CYS E 678 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 697 " distance=2.03 Simple disulfide: pdb=" SG CYS F 29 " - pdb=" SG CYS F 38 " distance=2.03 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 650 " - pdb=" SG CYS F 678 " distance=2.03 Simple disulfide: pdb=" SG CYS F 652 " - pdb=" SG CYS F 697 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=2, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " 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 g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG C 801 " - " ASN C 71 " " NAG C 802 " - " ASN C 197 " " NAG D 801 " - " ASN D 71 " " NAG D 802 " - " ASN D 197 " " NAG D 803 " - " ASN D 276 " " NAG D 804 " - " ASN D 292 " " NAG E 801 " - " ASN E 71 " " NAG E 802 " - " ASN E 197 " " NAG F 801 " - " ASN F 71 " " NAG F 802 " - " ASN F 197 " " NAG F 803 " - " ASN F 276 " " NAG F 804 " - " ASN F 292 " " NAG G 1 " - " ASN C 248 " " NAG H 1 " - " ASN C 253 " " NAG I 1 " - " ASN C 276 " " NAG J 1 " - " ASN C 292 " " NAG K 1 " - " ASN C 399 " " NAG L 1 " - " ASN C 414 " " NAG M 1 " - " ASN C 425 " " NAG N 1 " - " ASN C 508 " " NAG O 1 " - " ASN D 248 " " NAG P 1 " - " ASN D 253 " " NAG Q 1 " - " ASN D 399 " " NAG R 1 " - " ASN D 414 " " NAG S 1 " - " ASN D 425 " " NAG T 1 " - " ASN D 508 " " NAG U 1 " - " ASN E 248 " " NAG V 1 " - " ASN E 253 " " NAG W 1 " - " ASN E 276 " " NAG X 1 " - " ASN E 292 " " NAG Y 1 " - " ASN E 399 " " NAG Z 1 " - " ASN E 414 " " NAG a 1 " - " ASN E 425 " " NAG b 1 " - " ASN E 508 " " NAG c 1 " - " ASN F 248 " " NAG d 1 " - " ASN F 253 " " NAG e 1 " - " ASN F 399 " " NAG f 1 " - " ASN F 414 " " NAG g 1 " - " ASN F 425 " " NAG h 1 " - " ASN F 508 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.68 Conformation dependent library (CDL) restraints added in 3.1 seconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5108 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 39 sheets defined 9.9% alpha, 10.3% beta 65 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 8.18 Creating SS restraints... Processing helix chain 'C' and resid 93 through 99 removed outlier: 3.580A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.555A pdb=" N THR C 119 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 121 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 269 through 275 removed outlier: 4.197A pdb=" N TRP C 274 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 4.160A pdb=" N HIS C 407 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 454 removed outlier: 3.584A pdb=" N TRP C 453 " --> pdb=" O GLY C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 632 Processing helix chain 'C' and resid 633 through 636 Processing helix chain 'C' and resid 655 through 664 Processing helix chain 'D' and resid 93 through 99 removed outlier: 3.723A pdb=" N GLN D 97 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 235 through 246 removed outlier: 3.699A pdb=" N TRP D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.928A pdb=" N TRP D 274 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 4.430A pdb=" N SER D 404 " --> pdb=" O THR D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 454 Processing helix chain 'D' and resid 627 through 632 removed outlier: 3.536A pdb=" N PHE D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 636 Processing helix chain 'D' and resid 655 through 664 Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 116 through 121 removed outlier: 3.611A pdb=" N THR E 119 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL E 121 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 246 Processing helix chain 'E' and resid 269 through 275 removed outlier: 4.226A pdb=" N TRP E 274 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 406 Processing helix chain 'E' and resid 450 through 454 removed outlier: 3.689A pdb=" N TRP E 453 " --> pdb=" O GLY E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 632 Processing helix chain 'E' and resid 633 through 636 Processing helix chain 'E' and resid 655 through 664 Processing helix chain 'F' and resid 93 through 99 removed outlier: 3.772A pdb=" N GLN F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'F' and resid 235 through 246 removed outlier: 3.643A pdb=" N TRP F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU F 245 " --> pdb=" O LYS F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 removed outlier: 3.985A pdb=" N TRP F 274 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 407 removed outlier: 4.421A pdb=" N SER F 404 " --> pdb=" O THR F 401 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS F 407 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 454 Processing helix chain 'F' and resid 543 through 547 Processing helix chain 'F' and resid 627 through 632 Processing helix chain 'F' and resid 633 through 636 Processing helix chain 'F' and resid 651 through 664 removed outlier: 3.809A pdb=" N SER F 656 " --> pdb=" O CYS F 652 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP F 657 " --> pdb=" O GLU F 653 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHE F 658 " --> pdb=" O SER F 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.837A pdb=" N LEU C 57 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 81 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN C 106 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 129 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 154 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 153 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 177 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 186 through 187 removed outlier: 3.862A pdb=" N LEU C 187 " --> pdb=" O GLU C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 199 through 200 Processing sheet with id=AA4, first strand: chain 'C' and resid 226 through 228 removed outlier: 6.939A pdb=" N LEU C 227 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU C 254 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU C 280 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 462 " --> pdb=" O ARG C 485 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET C 487 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU C 486 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE C 592 " --> pdb=" O ASN C 617 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 616 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AA6, first strand: chain 'C' and resid 313 through 314 removed outlier: 4.053A pdb=" N LEU C 314 " --> pdb=" O ASN C 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 396 through 397 Processing sheet with id=AA8, first strand: chain 'C' and resid 445 through 447 removed outlier: 6.725A pdb=" N GLN C 446 " --> pdb=" O GLN C 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 648 through 649 removed outlier: 7.320A pdb=" N PHE C 648 " --> pdb=" O ASN C 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.800A pdb=" N LEU D 57 " --> pdb=" O ASP D 82 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 106 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 152 through 154 removed outlier: 6.695A pdb=" N LEU D 153 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU D 177 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU D 227 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU D 254 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 187 removed outlier: 3.670A pdb=" N LEU D 187 " --> pdb=" O GLU D 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 199 through 200 Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 264 Processing sheet with id=AB6, first strand: chain 'D' and resid 313 through 314 removed outlier: 4.111A pdb=" N LEU D 314 " --> pdb=" O ASN D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.981A pdb=" N LEU D 413 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AB9, first strand: chain 'D' and resid 445 through 447 removed outlier: 7.530A pdb=" N GLN D 446 " --> pdb=" O GLN D 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 461 through 463 removed outlier: 4.088A pdb=" N MET D 487 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 592 " --> pdb=" O ASN D 617 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 648 through 649 removed outlier: 7.181A pdb=" N PHE D 648 " --> pdb=" O ASN D 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.876A pdb=" N LEU E 57 " --> pdb=" O ASP E 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 104 through 106 removed outlier: 6.747A pdb=" N LEU E 153 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU E 177 " --> pdb=" O ASP E 204 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET E 487 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU E 486 " --> pdb=" O ASP E 513 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP E 537 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE E 592 " --> pdb=" O ASN E 617 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU E 616 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 186 through 187 removed outlier: 3.704A pdb=" N LEU E 187 " --> pdb=" O GLU E 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 199 through 200 Processing sheet with id=AC7, first strand: chain 'E' and resid 263 through 264 Processing sheet with id=AC8, first strand: chain 'E' and resid 313 through 314 removed outlier: 4.206A pdb=" N LEU E 314 " --> pdb=" O ASN E 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 396 through 397 Processing sheet with id=AD1, first strand: chain 'E' and resid 445 through 447 removed outlier: 6.598A pdb=" N GLN E 446 " --> pdb=" O GLN E 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 648 through 649 removed outlier: 7.216A pdb=" N PHE E 648 " --> pdb=" O ASN E 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 35 through 37 removed outlier: 6.548A pdb=" N ALA F 36 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F 57 " --> pdb=" O ASP F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 104 through 106 removed outlier: 6.475A pdb=" N LEU F 153 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU F 177 " --> pdb=" O ASP F 204 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU F 227 " --> pdb=" O SER F 255 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU F 254 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 186 through 187 removed outlier: 3.668A pdb=" N LEU F 187 " --> pdb=" O GLU F 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 199 through 200 Processing sheet with id=AD7, first strand: chain 'F' and resid 263 through 264 Processing sheet with id=AD8, first strand: chain 'F' and resid 313 through 314 removed outlier: 4.154A pdb=" N LEU F 314 " --> pdb=" O ASN F 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'F' and resid 396 through 397 Processing sheet with id=AE1, first strand: chain 'F' and resid 436 through 438 removed outlier: 6.999A pdb=" N LEU F 437 " --> pdb=" O TYR F 463 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET F 487 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU F 536 " --> pdb=" O ASN F 569 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE F 592 " --> pdb=" O ASN F 617 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU F 616 " --> pdb=" O ASP F 642 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 445 through 447 removed outlier: 7.411A pdb=" N GLN F 446 " --> pdb=" O GLN F 471 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU F 470 " --> pdb=" O LYS F 494 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 648 through 649 removed outlier: 7.244A pdb=" N PHE F 648 " --> pdb=" O ASN F 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 221 hydrogen bonds defined for protein. 552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 130 hydrogen bonds 260 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 10.92 Time building geometry restraints manager: 12.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7508 1.34 - 1.46: 5415 1.46 - 1.57: 13380 1.57 - 1.69: 322 1.69 - 1.81: 72 Bond restraints: 26697 Sorted by residual: bond pdb=" N TRP D 547 " pdb=" CA TRP D 547 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N LYS E 336 " pdb=" CA LYS E 336 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.31e+00 bond pdb=" N ILE E 46 " pdb=" CA ILE E 46 " ideal model delta sigma weight residual 1.461 1.476 -0.015 1.23e-02 6.61e+03 1.51e+00 bond pdb=" C1 NAG D 803 " pdb=" C2 NAG D 803 " ideal model delta sigma weight residual 1.526 1.550 -0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C1 NAG c 1 " pdb=" C2 NAG c 1 " ideal model delta sigma weight residual 1.526 1.549 -0.023 2.00e-02 2.50e+03 1.32e+00 ... (remaining 26692 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.22: 1673 107.22 - 114.06: 16153 114.06 - 120.90: 10506 120.90 - 127.75: 8210 127.75 - 134.59: 447 Bond angle restraints: 36989 Sorted by residual: angle pdb=" CA LEU C 394 " pdb=" CB LEU C 394 " pdb=" CG LEU C 394 " ideal model delta sigma weight residual 116.30 128.16 -11.86 3.50e+00 8.16e-02 1.15e+01 angle pdb=" CA LEU F 543 " pdb=" CB LEU F 543 " pdb=" CG LEU F 543 " ideal model delta sigma weight residual 116.30 127.27 -10.97 3.50e+00 8.16e-02 9.82e+00 angle pdb=" C1 NAG D 803 " pdb=" O5 NAG D 803 " pdb=" C5 NAG D 803 " ideal model delta sigma weight residual 113.34 118.65 -5.31 1.74e+00 3.30e-01 9.32e+00 angle pdb=" CA LEU D 394 " pdb=" CB LEU D 394 " pdb=" CG LEU D 394 " ideal model delta sigma weight residual 116.30 126.98 -10.68 3.50e+00 8.16e-02 9.32e+00 angle pdb=" C2 NAG D 803 " pdb=" C3 NAG D 803 " pdb=" C4 NAG D 803 " ideal model delta sigma weight residual 110.39 113.84 -3.45 1.16e+00 7.50e-01 8.92e+00 ... (remaining 36984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 15306 35.45 - 70.90: 325 70.90 - 106.35: 52 106.35 - 141.79: 1 141.79 - 177.24: 8 Dihedral angle restraints: 15692 sinusoidal: 7868 harmonic: 7824 Sorted by residual: dihedral pdb=" CB CYS F 652 " pdb=" SG CYS F 652 " pdb=" SG CYS F 697 " pdb=" CB CYS F 697 " ideal model delta sinusoidal sigma weight residual -86.00 -175.22 89.22 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS E 96 " pdb=" SG CYS E 96 " pdb=" SG CYS E 123 " pdb=" CB CYS E 123 " ideal model delta sinusoidal sigma weight residual -86.00 -142.57 56.57 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" C1 NAG D 803 " pdb=" C5 NAG D 803 " pdb=" O5 NAG D 803 " pdb=" C4 NAG D 803 " ideal model delta sinusoidal sigma weight residual -50.00 53.93 -103.93 1 2.00e+01 2.50e-03 2.98e+01 ... (remaining 15689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4265 0.063 - 0.126: 343 0.126 - 0.190: 28 0.190 - 0.253: 11 0.253 - 0.316: 3 Chirality restraints: 4650 Sorted by residual: chirality pdb=" C1 NAG F 802 " pdb=" ND2 ASN F 197 " pdb=" C2 NAG F 802 " pdb=" O5 NAG F 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 292 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1 NAG F 804 " pdb=" ND2 ASN F 292 " pdb=" C2 NAG F 804 " pdb=" O5 NAG F 804 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 4647 not shown) Planarity restraints: 4058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 50 " -0.039 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO C 51 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 508 " -0.019 2.00e-02 2.50e+03 1.80e-02 4.06e+00 pdb=" CG ASN D 508 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 508 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 508 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 399 " -0.017 2.00e-02 2.50e+03 1.58e-02 3.12e+00 pdb=" CG ASN C 399 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN C 399 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 399 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " -0.015 2.00e-02 2.50e+03 ... (remaining 4055 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 979 2.69 - 3.24: 24782 3.24 - 3.80: 43779 3.80 - 4.35: 56779 4.35 - 4.90: 88672 Nonbonded interactions: 214991 Sorted by model distance: nonbonded pdb=" OG SER D 247 " pdb=" O GLY D 271 " model vdw 2.140 2.440 nonbonded pdb=" O LEU C 171 " pdb=" OG SER C 198 " model vdw 2.181 2.440 nonbonded pdb=" O LEU C 246 " pdb=" OG1 THR C 249 " model vdw 2.201 2.440 nonbonded pdb=" OG SER C 113 " pdb=" O2' U B 50 " model vdw 2.214 2.440 nonbonded pdb=" O4 U A 80 " pdb=" N1 A B 11 " model vdw 2.216 3.120 ... (remaining 214986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 44 or resid 46 through 85)) selection = (chain 'B' and (resid 6 through 45 or resid 47 through 86)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 29 through 336 or resid 343 through 698 or resid 801 throu \ gh 802)) selection = chain 'E' selection = (chain 'F' and (resid 29 through 336 or resid 343 through 698 or resid 801 throu \ gh 802)) } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 162 5.49 5 S 56 5.16 5 C 15795 2.51 5 N 4273 2.21 5 O 5562 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.320 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: 0.020 Extract box with map and model: 6.900 Check model and map are aligned: 0.400 Process input model: 72.330 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Set scattering table: 0.240 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 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 : 0.002 0.036 26697 Z= 0.128 Angle : 0.521 11.855 36989 Z= 0.259 Chirality : 0.040 0.316 4650 Planarity : 0.003 0.060 4018 Dihedral : 15.513 177.243 10536 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.73 (0.16), residues: 2638 helix: -1.05 (0.38), residues: 208 sheet: -1.72 (0.26), residues: 430 loop : -1.07 (0.14), residues: 2000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 2.762 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.3144 time to fit residues: 81.2320 Evaluate side-chains 107 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 3.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 219 optimal weight: 30.0000 chunk 84 optimal weight: 0.0470 chunk 133 optimal weight: 0.0970 chunk 163 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 overall best weight: 3.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 446 GLN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN D 367 ASN D 467 ASN ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN E 433 GLN E 467 ASN E 471 GLN ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 GLN ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 26697 Z= 0.235 Angle : 0.607 12.686 36989 Z= 0.299 Chirality : 0.042 0.335 4650 Planarity : 0.004 0.058 4018 Dihedral : 13.631 179.953 5290 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.18 % Favored : 93.71 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.85 (0.16), residues: 2638 helix: -1.21 (0.37), residues: 202 sheet: -1.73 (0.26), residues: 446 loop : -1.16 (0.14), residues: 1990 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 2.809 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 121 average time/residue: 0.2964 time to fit residues: 65.2155 Evaluate side-chains 107 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 2.702 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2497 time to fit residues: 11.1488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 211 optimal weight: 30.0000 chunk 173 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 226 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 204 optimal weight: 8.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN C 433 GLN C 446 GLN ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 HIS C 660 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN D 564 HIS ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 HIS ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 HIS ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN E 663 ASN E 664 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 ASN ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 26697 Z= 0.446 Angle : 0.849 11.911 36989 Z= 0.428 Chirality : 0.050 0.427 4650 Planarity : 0.005 0.073 4018 Dihedral : 14.978 176.445 5290 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 29.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.10 % Favored : 90.71 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.37 (0.16), residues: 2638 helix: -1.30 (0.36), residues: 188 sheet: -1.88 (0.26), residues: 430 loop : -1.64 (0.13), residues: 2020 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 92 time to evaluate : 2.931 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 26 residues processed: 137 average time/residue: 0.3108 time to fit residues: 77.0270 Evaluate side-chains 94 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 68 time to evaluate : 3.092 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2435 time to fit residues: 15.6538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 242 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 663 ASN D 664 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 ASN ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 26697 Z= 0.276 Angle : 0.636 11.006 36989 Z= 0.324 Chirality : 0.044 0.413 4650 Planarity : 0.004 0.059 4018 Dihedral : 14.759 178.298 5290 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.88 % Favored : 91.96 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.34 (0.16), residues: 2638 helix: -1.22 (0.37), residues: 188 sheet: -1.92 (0.25), residues: 440 loop : -1.61 (0.13), residues: 2010 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 84 time to evaluate : 2.868 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 16 residues processed: 120 average time/residue: 0.3119 time to fit residues: 68.1770 Evaluate side-chains 90 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 2.960 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2295 time to fit residues: 10.5247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 40.0000 chunk 153 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 201 optimal weight: 30.0000 chunk 111 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 68 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 26697 Z= 0.355 Angle : 0.724 11.776 36989 Z= 0.365 Chirality : 0.047 0.426 4650 Planarity : 0.004 0.060 4018 Dihedral : 15.093 176.997 5290 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.12 % Favored : 89.73 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.63 (0.16), residues: 2638 helix: -1.14 (0.37), residues: 188 sheet: -2.20 (0.25), residues: 420 loop : -1.84 (0.13), residues: 2030 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 80 time to evaluate : 2.889 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 115 average time/residue: 0.3274 time to fit residues: 66.8397 Evaluate side-chains 95 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 2.700 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2446 time to fit residues: 13.9593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 30.0000 chunk 243 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 158 optimal weight: 0.4980 chunk 66 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 224 optimal weight: 30.0000 chunk 125 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 overall best weight: 6.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN D 86 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 HIS ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 26697 Z= 0.381 Angle : 0.739 11.704 36989 Z= 0.373 Chirality : 0.047 0.448 4650 Planarity : 0.004 0.062 4018 Dihedral : 15.307 177.345 5290 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 28.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.82 % Favored : 90.03 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.75 (0.15), residues: 2638 helix: -1.06 (0.37), residues: 188 sheet: -2.23 (0.25), residues: 418 loop : -1.96 (0.13), residues: 2032 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 72 time to evaluate : 2.758 Fit side-chains outliers start: 48 outliers final: 23 residues processed: 113 average time/residue: 0.3052 time to fit residues: 62.6303 Evaluate side-chains 87 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2432 time to fit residues: 14.0410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 30.0000 chunk 30 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 269 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 663 ASN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 26697 Z= 0.249 Angle : 0.630 11.912 36989 Z= 0.320 Chirality : 0.045 0.428 4650 Planarity : 0.004 0.061 4018 Dihedral : 15.135 179.051 5290 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.87 % Favored : 90.98 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.55 (0.16), residues: 2638 helix: -0.58 (0.42), residues: 160 sheet: -2.20 (0.25), residues: 408 loop : -1.82 (0.13), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 97 average time/residue: 0.3442 time to fit residues: 58.6624 Evaluate side-chains 78 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 2.767 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2598 time to fit residues: 9.9867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 133 optimal weight: 0.0010 chunk 25 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN D 110 ASN ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 ASN ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 26697 Z= 0.153 Angle : 0.595 11.876 36989 Z= 0.294 Chirality : 0.044 0.378 4650 Planarity : 0.004 0.060 4018 Dihedral : 14.799 179.376 5290 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.37 % Favored : 93.48 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.30 (0.16), residues: 2638 helix: -0.52 (0.42), residues: 160 sheet: -2.12 (0.26), residues: 392 loop : -1.61 (0.13), residues: 2086 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 98 average time/residue: 0.3349 time to fit residues: 58.1328 Evaluate side-chains 80 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 2.708 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2539 time to fit residues: 5.4045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 227 optimal weight: 20.0000 chunk 237 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 ASN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 26697 Z= 0.286 Angle : 0.654 12.137 36989 Z= 0.328 Chirality : 0.045 0.413 4650 Planarity : 0.004 0.061 4018 Dihedral : 14.981 179.486 5290 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.59 % Favored : 90.26 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.47 (0.16), residues: 2638 helix: -0.63 (0.41), residues: 170 sheet: -2.08 (0.26), residues: 402 loop : -1.77 (0.13), residues: 2066 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 2.854 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 0.3292 time to fit residues: 51.0032 Evaluate side-chains 78 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 2.740 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3256 time to fit residues: 8.1686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 2.9990 chunk 265 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 278 optimal weight: 10.0000 chunk 256 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 26697 Z= 0.264 Angle : 0.639 11.995 36989 Z= 0.323 Chirality : 0.045 0.417 4650 Planarity : 0.004 0.061 4018 Dihedral : 15.086 179.398 5290 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.91 % Favored : 90.94 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.53 (0.16), residues: 2638 helix: -0.76 (0.40), residues: 170 sheet: -2.13 (0.26), residues: 408 loop : -1.79 (0.13), residues: 2060 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 2.694 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 76 average time/residue: 0.3257 time to fit residues: 45.7646 Evaluate side-chains 71 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.755 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 68 optimal weight: 40.0000 chunk 204 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 93 optimal weight: 40.0000 chunk 228 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.062925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.049653 restraints weight = 218373.834| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 5.92 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 26697 Z= 0.188 Angle : 0.593 11.837 36989 Z= 0.297 Chirality : 0.043 0.393 4650 Planarity : 0.004 0.060 4018 Dihedral : 14.913 179.549 5290 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.61 % Favored : 91.24 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.38 (0.16), residues: 2638 helix: -0.68 (0.40), residues: 170 sheet: -2.06 (0.26), residues: 412 loop : -1.68 (0.13), residues: 2056 =============================================================================== Job complete usr+sys time: 4161.39 seconds wall clock time: 79 minutes 4.04 seconds (4744.04 seconds total)