Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 15:48:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/04_2023/7wm4_32599.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/04_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_32599/04_2023/7wm4_32599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/04_2023/7wm4_32599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/04_2023/7wm4_32599.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/04_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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 13.06, per 1000 atoms: 0.51 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: 12.97 Conformation dependent library (CDL) restraints added in 3.7 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: 7.75 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: 9.85 Time building geometry restraints manager: 13.61 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=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" C1 NAG D 803 " pdb=" O5 NAG D 803 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C1 NAG D 804 " pdb=" O5 NAG D 804 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.27e+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=" 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=" C ASN C 285 " pdb=" N ASN C 286 " pdb=" CA ASN C 286 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.78e+00 angle pdb=" C ASN E 285 " pdb=" N ASN E 286 " pdb=" CA ASN E 286 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.61e+00 ... (remaining 36984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 14767 35.45 - 70.90: 324 70.90 - 106.35: 44 106.35 - 141.79: 1 141.79 - 177.24: 8 Dihedral angle restraints: 15144 sinusoidal: 7320 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=" CB CYS E 652 " pdb=" SG CYS E 652 " pdb=" SG CYS E 697 " pdb=" CB CYS E 697 " ideal model delta sinusoidal sigma weight residual 93.00 52.41 40.59 1 1.00e+01 1.00e-02 2.31e+01 ... (remaining 15141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4169 0.063 - 0.126: 413 0.126 - 0.190: 39 0.190 - 0.253: 13 0.253 - 0.316: 16 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=" C5 BMA g 3 " pdb=" C4 BMA g 3 " pdb=" C6 BMA g 3 " pdb=" O5 BMA g 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+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 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.930 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 73.000 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 : 0.003 0.056 26697 Z= 0.191 Angle : 0.630 11.855 36989 Z= 0.280 Chirality : 0.045 0.316 4650 Planarity : 0.003 0.060 4018 Dihedral : 15.609 177.243 9988 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.96 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 : 2.797 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.3066 time to fit residues: 79.3296 Evaluate side-chains 107 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.521 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2884 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 26697 Z= 0.223 Angle : 0.602 12.122 36989 Z= 0.288 Chirality : 0.042 0.351 4650 Planarity : 0.003 0.059 4018 Dihedral : 13.577 179.813 4742 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.88 % Favored : 94.01 % Rotamer Outliers : 1.05 % 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: -1.81 (0.16), residues: 2638 helix: -1.17 (0.37), residues: 202 sheet: -1.71 (0.26), residues: 446 loop : -1.13 (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 130 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 2.757 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 121 average time/residue: 0.2941 time to fit residues: 64.2142 Evaluate side-chains 105 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 2.740 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2370 time to fit residues: 9.6696 ------------------------------------------------------------------------------- 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: 4.9990 chunk 78 optimal weight: 6.9990 chunk 211 optimal weight: 40.0000 chunk 173 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 226 optimal weight: 0.8980 chunk 252 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN C 446 GLN C 471 GLN ** 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 D 110 ASN ** 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 664 GLN E 109 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 GLN ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 HIS ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 260 GLN ** 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 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 ASN ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 26697 Z= 0.320 Angle : 0.722 11.628 36989 Z= 0.352 Chirality : 0.046 0.335 4650 Planarity : 0.004 0.060 4018 Dihedral : 14.497 177.590 4742 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.54 % Favored : 92.30 % 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: -2.15 (0.16), residues: 2638 helix: -1.18 (0.36), residues: 202 sheet: -1.76 (0.26), residues: 438 loop : -1.46 (0.13), residues: 1998 *********************** 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: 46 poor density : 99 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 17 residues processed: 134 average time/residue: 0.3027 time to fit residues: 73.2988 Evaluate side-chains 100 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 2.706 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2325 time to fit residues: 10.9679 ------------------------------------------------------------------------------- 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: 7.9990 chunk 132 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 121 optimal weight: 0.4980 chunk 171 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 270 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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 175 GLN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 660 ASN D 86 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 HIS ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN E 419 HIS ** 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 231 ASN F 258 ASN ** F 260 GLN ** 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 ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 26697 Z= 0.296 Angle : 0.683 16.458 36989 Z= 0.334 Chirality : 0.045 0.340 4650 Planarity : 0.004 0.058 4018 Dihedral : 14.831 178.062 4742 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.88 % Favored : 91.96 % Rotamer Outliers : 2.09 % 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: -2.29 (0.16), residues: 2638 helix: -1.21 (0.37), residues: 188 sheet: -1.92 (0.25), residues: 440 loop : -1.56 (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 145 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 93 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 25 residues processed: 138 average time/residue: 0.2968 time to fit residues: 72.5395 Evaluate side-chains 104 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 2.736 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2455 time to fit residues: 15.1040 ------------------------------------------------------------------------------- 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: 30.0000 chunk 153 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 201 optimal weight: 30.0000 chunk 111 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 187 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 68 optimal weight: 50.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- 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 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 419 HIS ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN ** 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 118 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 208 ASN ** 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** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** F 235 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 585 ASN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.064 26697 Z= 0.519 Angle : 0.961 12.207 36989 Z= 0.466 Chirality : 0.052 0.389 4650 Planarity : 0.006 0.062 4018 Dihedral : 15.835 176.662 4742 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 36.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.94 % Favored : 87.87 % Rotamer Outliers : 2.21 % 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: -2.85 (0.15), residues: 2638 helix: -1.29 (0.36), residues: 188 sheet: -2.26 (0.24), residues: 450 loop : -2.01 (0.13), residues: 2000 *********************** 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 129 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 74 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 28 residues processed: 120 average time/residue: 0.3081 time to fit residues: 66.8491 Evaluate side-chains 91 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 63 time to evaluate : 2.745 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2361 time to fit residues: 16.2690 ------------------------------------------------------------------------------- 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: 50.0000 chunk 243 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 chunk 66 optimal weight: 30.0000 chunk 270 optimal weight: 10.0000 chunk 224 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 overall best weight: 4.6586 ------------------------------------------------------------------------------- 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 495 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 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 541 ASN ** 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 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 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 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: 0.7685 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 26697 Z= 0.277 Angle : 0.705 13.067 36989 Z= 0.342 Chirality : 0.045 0.337 4650 Planarity : 0.004 0.060 4018 Dihedral : 15.462 178.899 4742 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.76 % Favored : 91.09 % Rotamer Outliers : 1.53 % 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: -2.65 (0.16), residues: 2638 helix: -0.80 (0.40), residues: 160 sheet: -2.30 (0.24), residues: 428 loop : -1.86 (0.13), residues: 2050 *********************** 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 116 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 78 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 110 average time/residue: 0.3353 time to fit residues: 66.1643 Evaluate side-chains 91 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 3.106 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2965 time to fit residues: 13.0875 ------------------------------------------------------------------------------- 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: 20.0000 chunk 30 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 197 optimal weight: 30.0000 chunk 153 optimal weight: 0.6980 chunk 228 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 269 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 593 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 541 ASN ** 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 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 235 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 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 26697 Z= 0.300 Angle : 0.718 12.195 36989 Z= 0.347 Chirality : 0.045 0.334 4650 Planarity : 0.004 0.060 4018 Dihedral : 15.471 179.993 4742 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 27.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.73 % Favored : 89.12 % Rotamer Outliers : 0.80 % 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: -2.78 (0.16), residues: 2638 helix: -1.28 (0.36), residues: 188 sheet: -2.32 (0.24), residues: 438 loop : -1.92 (0.13), residues: 2012 *********************** 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 95 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 93 average time/residue: 0.3201 time to fit residues: 53.5139 Evaluate side-chains 80 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 2.702 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2370 time to fit residues: 8.2374 ------------------------------------------------------------------------------- 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: 5.9990 chunk 161 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 212 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN C 660 ASN ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN E 40 HIS ** 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 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 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 26697 Z= 0.150 Angle : 0.632 12.312 36989 Z= 0.301 Chirality : 0.043 0.345 4650 Planarity : 0.004 0.059 4018 Dihedral : 15.083 179.487 4742 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.44 % Favored : 93.40 % Rotamer Outliers : 0.40 % 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: -2.42 (0.16), residues: 2638 helix: -0.85 (0.39), residues: 172 sheet: -2.17 (0.26), residues: 394 loop : -1.68 (0.13), residues: 2072 *********************** 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 102 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 0.3515 time to fit residues: 60.2305 Evaluate side-chains 85 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 2.778 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2311 time to fit residues: 5.4009 ------------------------------------------------------------------------------- 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: 3.9990 chunk 258 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 151 optimal weight: 0.0670 chunk 109 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 77 optimal weight: 40.0000 chunk 227 optimal weight: 30.0000 chunk 237 optimal weight: 7.9990 chunk 250 optimal weight: 0.0970 overall best weight: 3.2322 ------------------------------------------------------------------------------- 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 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 593 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 235 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: 0.7648 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 26697 Z= 0.215 Angle : 0.640 12.155 36989 Z= 0.307 Chirality : 0.043 0.342 4650 Planarity : 0.004 0.059 4018 Dihedral : 15.113 179.189 4742 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.76 % Favored : 91.09 % Rotamer Outliers : 0.40 % 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: -2.43 (0.16), residues: 2638 helix: -0.87 (0.39), residues: 172 sheet: -2.04 (0.26), residues: 394 loop : -1.73 (0.13), residues: 2072 *********************** 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 87 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 87 average time/residue: 0.3378 time to fit residues: 52.3517 Evaluate side-chains 79 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 2.863 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4008 time to fit residues: 6.7654 ------------------------------------------------------------------------------- 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: 3.9990 chunk 265 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 256 optimal weight: 20.0000 chunk 222 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 170 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 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN ** 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 235 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 26697 Z= 0.192 Angle : 0.632 12.143 36989 Z= 0.303 Chirality : 0.042 0.341 4650 Planarity : 0.004 0.059 4018 Dihedral : 15.058 179.954 4742 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.11 % Favored : 91.74 % Rotamer Outliers : 0.28 % 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: -0.79 (0.40), residues: 170 sheet: -2.03 (0.26), residues: 394 loop : -1.68 (0.13), residues: 2074 ********************** 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 85 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 82 average time/residue: 0.3294 time to fit residues: 49.7165 Evaluate side-chains 76 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2475 time to fit residues: 5.3267 ------------------------------------------------------------------------------- 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: 3.9990 chunk 236 optimal weight: 8.9990 chunk 68 optimal weight: 50.0000 chunk 204 optimal weight: 0.1980 chunk 32 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 222 optimal weight: 30.0000 chunk 93 optimal weight: 40.0000 chunk 228 optimal weight: 30.0000 chunk 28 optimal weight: 0.0970 chunk 40 optimal weight: 6.9990 overall best weight: 3.8584 ------------------------------------------------------------------------------- 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 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN ** D 86 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 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.061018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.048117 restraints weight = 222443.595| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 5.71 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 26697 Z= 0.241 Angle : 0.658 12.139 36989 Z= 0.316 Chirality : 0.043 0.337 4650 Planarity : 0.004 0.060 4018 Dihedral : 15.131 179.997 4742 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.70 % Favored : 90.14 % 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: -2.43 (0.16), residues: 2638 helix: -0.71 (0.40), residues: 170 sheet: -1.92 (0.27), residues: 368 loop : -1.78 (0.13), residues: 2100 =============================================================================== Job complete usr+sys time: 3787.29 seconds wall clock time: 72 minutes 18.60 seconds (4338.60 seconds total)