Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 20:51:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/10_2023/7wg9_32481.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/10_2023/7wg9_32481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/10_2023/7wg9_32481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/10_2023/7wg9_32481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/10_2023/7wg9_32481.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg9_32481/10_2023/7wg9_32481.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16388 2.51 5 N 4228 2.21 5 O 5036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1137": "OD1" <-> "OD2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 617": "OE1" <-> "OE2" Residue "C PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1109": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 25769 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 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: 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: 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 12.66, per 1000 atoms: 0.49 Number of scatterers: 25769 At special positions: 0 Unit cell: (141.24, 146.59, 200.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 5036 8.00 N 4228 7.00 C 16388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.04 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.02 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.02 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " 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 L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 280 " " NAG A1304 " - " ASN A 329 " " NAG A1305 " - " ASN A 341 " " NAG A1306 " - " ASN A 601 " " NAG A1307 " - " ASN A 614 " " NAG A1308 " - " ASN A 655 " " NAG A1309 " - " ASN A 707 " " NAG A1310 " - " ASN A1072 " " NAG A1311 " - " ASN A 163 " " NAG A1312 " - " ASN A 232 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 280 " " NAG B1304 " - " ASN B 329 " " NAG B1305 " - " ASN B 341 " " NAG B1306 " - " ASN B 614 " " NAG B1307 " - " ASN B 655 " " NAG B1308 " - " ASN B 707 " " NAG B1309 " - " ASN B1072 " " NAG B1310 " - " ASN B 163 " " NAG B1311 " - " ASN B 601 " " NAG B1312 " - " ASN B 232 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 280 " " NAG C1304 " - " ASN C 329 " " NAG C1305 " - " ASN C 341 " " NAG C1306 " - " ASN C 614 " " NAG C1307 " - " ASN C 655 " " NAG C1308 " - " ASN C1072 " " NAG C1309 " - " ASN C 163 " " NAG C1310 " - " ASN C 232 " " NAG C1311 " - " ASN C 601 " " NAG D 1 " - " ASN A 715 " " NAG E 1 " - " ASN A 799 " " NAG F 1 " - " ASN A1096 " " NAG G 1 " - " ASN A1132 " " NAG H 1 " - " ASN B 715 " " NAG I 1 " - " ASN B 799 " " NAG J 1 " - " ASN B1096 " " NAG K 1 " - " ASN B1132 " " NAG L 1 " - " ASN C 707 " " NAG M 1 " - " ASN C 715 " " NAG N 1 " - " ASN C 799 " " NAG O 1 " - " ASN C1096 " " NAG P 1 " - " ASN C1132 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.21 Conformation dependent library (CDL) restraints added in 3.7 seconds 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 44 sheets defined 25.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.661A pdb=" N HIS A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 147' Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.558A pdb=" N VAL A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.689A pdb=" N VAL A 618 " --> pdb=" O CYS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 removed outlier: 3.891A pdb=" N TYR A 739 " --> pdb=" O ASP A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.748A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 848 through 853 removed outlier: 3.553A pdb=" N LYS A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 889 removed outlier: 4.146A pdb=" N ALA A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 889' Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.879A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.866A pdb=" N VAL A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 Processing helix chain 'A' and resid 983 through 1032 removed outlier: 3.743A pdb=" N GLU A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1139 through 1146 removed outlier: 4.261A pdb=" N LEU A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.559A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.061A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 4.234A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 409 " --> pdb=" O ARG B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 618 removed outlier: 3.606A pdb=" N VAL B 618 " --> pdb=" O CYS B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.564A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 848 through 855 removed outlier: 4.292A pdb=" N LYS B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 854 " --> pdb=" O ALA B 850 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 882 Processing helix chain 'B' and resid 895 through 908 Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.635A pdb=" N VAL B 913 " --> pdb=" O THR B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 940 through 942 No H-bonds generated for 'chain 'B' and resid 940 through 942' Processing helix chain 'B' and resid 943 through 963 removed outlier: 4.339A pdb=" N VAL B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 982 Processing helix chain 'B' and resid 983 through 1030 removed outlier: 5.144A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1146 removed outlier: 4.655A pdb=" N GLU B1142 " --> pdb=" O PRO B1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.918A pdb=" N VAL C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 removed outlier: 3.738A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.503A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 5.133A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 741 removed outlier: 3.550A pdb=" N TYR C 739 " --> pdb=" O ASP C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 781 removed outlier: 4.145A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 848 through 852 Processing helix chain 'C' and resid 853 through 855 No H-bonds generated for 'chain 'C' and resid 853 through 855' Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.506A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 908 removed outlier: 3.623A pdb=" N ILE C 907 " --> pdb=" O ARG C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.809A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.882A pdb=" N THR C 939 " --> pdb=" O SER C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 942 No H-bonds generated for 'chain 'C' and resid 940 through 942' Processing helix chain 'C' and resid 943 through 963 removed outlier: 4.312A pdb=" N VAL C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.549A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 986 Processing helix chain 'C' and resid 987 through 1030 Processing helix chain 'C' and resid 1139 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.516A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 96 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN A 186 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 195 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE A 199 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP A 226 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE A 201 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.663A pdb=" N PHE A 43 " --> pdb=" O PHE B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.582A pdb=" N GLY A 107 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N VAL A 126 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N GLU A 167 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N ILE A 128 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR A 165 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL A 130 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASN A 163 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU A 132 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A 161 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN A 134 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 312 Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 326 removed outlier: 3.508A pdb=" N ARG A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 removed outlier: 3.603A pdb=" N CYS A 430 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.694A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 654 removed outlier: 4.619A pdb=" N THR A 694 " --> pdb=" O VAL A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.907A pdb=" N ALA A 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.828A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN A 715 " --> pdb=" O ALA A1068 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A1054 " --> pdb=" O GLY A1057 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.828A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN A 715 " --> pdb=" O ALA A1068 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 734 Processing sheet with id=AB7, first strand: chain 'A' and resid 1118 through 1123 removed outlier: 4.391A pdb=" N ALA A1085 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.661A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU B 96 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN B 186 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 225 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.610A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 317 removed outlier: 4.680A pdb=" N VAL B 593 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN B 315 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY B 591 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 611 " --> pdb=" O GLY B 592 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.726A pdb=" N ASN B 392 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 removed outlier: 7.327A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC6, first strand: chain 'B' and resid 471 through 472 removed outlier: 3.584A pdb=" N TYR B 471 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 487 " --> pdb=" O TYR B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 540 Processing sheet with id=AC8, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.022A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 709 through 713 Processing sheet with id=AD1, first strand: chain 'B' and resid 716 through 726 removed outlier: 3.559A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 732 through 734 Processing sheet with id=AD3, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 4.875A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.897A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 263 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 227 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 201 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 225 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.896A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.805A pdb=" N VAL C 130 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU C 132 " --> pdb=" O CYS C 164 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N GLN C 134 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N ASN C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 316 removed outlier: 4.651A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 648 " --> pdb=" O PHE C 641 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 324 removed outlier: 3.527A pdb=" N ILE C 324 " --> pdb=" O ASN C 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 352 through 356 removed outlier: 3.900A pdb=" N ALA C 433 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR C 374 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE2, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE3, first strand: chain 'C' and resid 549 through 552 Processing sheet with id=AE4, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.084A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 668 " --> pdb=" O ILE C 664 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 709 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 726 removed outlier: 3.648A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE8, first strand: chain 'C' and resid 1092 through 1095 958 hydrogen bonds defined for protein. 2625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.84 Time building geometry restraints manager: 10.96 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: 8186 1.34 - 1.47: 6584 1.47 - 1.59: 11424 1.59 - 1.71: 1 1.71 - 1.83: 147 Bond restraints: 26342 Sorted by residual: bond pdb=" CA LEU B 177 " pdb=" C LEU B 177 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.34e-02 5.57e+03 4.48e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.37e+00 bond pdb=" CB PRO C 525 " pdb=" CG PRO C 525 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.14e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 26337 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.41: 709 106.41 - 113.52: 14599 113.52 - 120.62: 10251 120.62 - 127.73: 10093 127.73 - 134.83: 178 Bond angle restraints: 35830 Sorted by residual: angle pdb=" CA TRP C 152 " pdb=" CB TRP C 152 " pdb=" CG TRP C 152 " ideal model delta sigma weight residual 113.60 120.35 -6.75 1.90e+00 2.77e-01 1.26e+01 angle pdb=" C ALA A 568 " pdb=" N ASP A 569 " pdb=" CA ASP A 569 " ideal model delta sigma weight residual 122.46 127.32 -4.86 1.41e+00 5.03e-01 1.19e+01 angle pdb=" C LYS B 97 " pdb=" N SER B 98 " pdb=" CA SER B 98 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.21e+00 angle pdb=" C ALA C 568 " pdb=" N ASP C 569 " pdb=" CA ASP C 569 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.52e+00 angle pdb=" CA CYS A 536 " pdb=" CB CYS A 536 " pdb=" SG CYS A 536 " ideal model delta sigma weight residual 114.40 121.10 -6.70 2.30e+00 1.89e-01 8.48e+00 ... (remaining 35825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 13737 17.69 - 35.38: 1187 35.38 - 53.07: 218 53.07 - 70.76: 59 70.76 - 88.45: 24 Dihedral angle restraints: 15225 sinusoidal: 5952 harmonic: 9273 Sorted by residual: dihedral pdb=" CB CYS B 289 " pdb=" SG CYS B 289 " pdb=" SG CYS B 299 " pdb=" CB CYS B 299 " ideal model delta sinusoidal sigma weight residual -86.00 -4.64 -81.36 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS B 478 " pdb=" SG CYS B 478 " pdb=" SG CYS B 486 " pdb=" CB CYS B 486 " ideal model delta sinusoidal sigma weight residual 93.00 173.47 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS C 478 " pdb=" SG CYS C 478 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 149.89 -56.89 1 1.00e+01 1.00e-02 4.36e+01 ... (remaining 15222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4135 0.112 - 0.225: 84 0.225 - 0.337: 3 0.337 - 0.449: 0 0.449 - 0.562: 1 Chirality restraints: 4223 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 707 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C1096 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C1132 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 4220 not shown) Planarity restraints: 4615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 227 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO C 228 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 206 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO B 207 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 227 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO B 228 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " -0.030 5.00e-02 4.00e+02 ... (remaining 4612 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 632 2.69 - 3.25: 25204 3.25 - 3.80: 39060 3.80 - 4.35: 49159 4.35 - 4.90: 83638 Nonbonded interactions: 197693 Sorted by model distance: nonbonded pdb=" OG SER B 436 " pdb=" OD2 ASP B 440 " model vdw 2.144 2.440 nonbonded pdb=" OG1 THR A 391 " pdb=" O GLU A 514 " model vdw 2.161 2.440 nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.181 2.440 nonbonded pdb=" NH1 ARG C1017 " pdb=" OD1 ASN C1021 " model vdw 2.211 2.520 nonbonded pdb=" O ASP B 440 " pdb=" ND2 ASN B 446 " model vdw 2.212 2.520 ... (remaining 197688 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 14 through 1146 or resid 1301 through 1311)) selection = (chain 'B' and (resid 14 through 1146 or resid 1301 through 1311)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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 group one per residue 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: 3.270 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: 0.030 Extract box with map and model: 9.020 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 66.450 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.240 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 0.102 26342 Z= 0.225 Angle : 0.615 9.831 35830 Z= 0.312 Chirality : 0.046 0.562 4223 Planarity : 0.004 0.073 4567 Dihedral : 13.911 88.449 9135 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3153 helix: 1.64 (0.21), residues: 662 sheet: -0.22 (0.20), residues: 625 loop : -1.62 (0.13), residues: 1866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.3845 time to fit residues: 298.6508 Evaluate side-chains 210 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.934 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 0.0770 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 249 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN C 134 GLN C 392 ASN C 899 GLN C 924 GLN ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26342 Z= 0.329 Angle : 0.670 10.119 35830 Z= 0.336 Chirality : 0.048 0.427 4223 Planarity : 0.004 0.058 4567 Dihedral : 4.582 31.039 3417 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.41 % Allowed : 9.06 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3153 helix: 1.89 (0.20), residues: 668 sheet: -0.26 (0.21), residues: 584 loop : -1.69 (0.13), residues: 1901 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 239 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 39 residues processed: 283 average time/residue: 0.3568 time to fit residues: 165.1963 Evaluate side-chains 231 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 2.931 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2565 time to fit residues: 21.9030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 289 optimal weight: 0.9990 chunk 312 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 286 optimal weight: 0.2980 chunk 98 optimal weight: 0.7980 chunk 232 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 ASN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN B 485 ASN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN C 125 ASN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26342 Z= 0.164 Angle : 0.565 10.021 35830 Z= 0.280 Chirality : 0.045 0.420 4223 Planarity : 0.004 0.062 4567 Dihedral : 4.336 30.618 3417 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.04 % Allowed : 12.01 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3153 helix: 2.36 (0.21), residues: 663 sheet: 0.04 (0.21), residues: 568 loop : -1.58 (0.13), residues: 1922 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 222 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 243 average time/residue: 0.3577 time to fit residues: 143.6215 Evaluate side-chains 197 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 2.989 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2453 time to fit residues: 8.5957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 32 optimal weight: 30.0000 chunk 138 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 ASN B1140 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN C 911 GLN C1003 GLN C1086 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26342 Z= 0.251 Angle : 0.588 10.886 35830 Z= 0.292 Chirality : 0.045 0.421 4223 Planarity : 0.004 0.064 4567 Dihedral : 4.358 29.842 3417 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.05 % Allowed : 13.63 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3153 helix: 2.20 (0.20), residues: 660 sheet: -0.01 (0.21), residues: 591 loop : -1.59 (0.13), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 218 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 25 residues processed: 254 average time/residue: 0.3612 time to fit residues: 152.8753 Evaluate side-chains 220 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 2.858 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2384 time to fit residues: 15.5777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 chunk 212 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 156 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN A 933 GLN B 146 HIS B 149 ASN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26342 Z= 0.222 Angle : 0.573 11.243 35830 Z= 0.284 Chirality : 0.045 0.430 4223 Planarity : 0.004 0.064 4567 Dihedral : 4.304 28.327 3417 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.29 % Allowed : 14.99 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3153 helix: 2.20 (0.20), residues: 666 sheet: 0.02 (0.21), residues: 579 loop : -1.56 (0.13), residues: 1908 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 205 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 231 average time/residue: 0.3450 time to fit residues: 134.0877 Evaluate side-chains 205 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 3.172 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2369 time to fit residues: 10.7814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 4.9990 chunk 276 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 255 optimal weight: 0.0270 chunk 142 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26342 Z= 0.188 Angle : 0.562 9.902 35830 Z= 0.277 Chirality : 0.045 0.424 4223 Planarity : 0.004 0.065 4567 Dihedral : 4.223 28.956 3417 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.01 % Allowed : 16.07 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3153 helix: 2.32 (0.20), residues: 665 sheet: 0.06 (0.21), residues: 597 loop : -1.51 (0.13), residues: 1891 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 220 average time/residue: 0.3429 time to fit residues: 126.6187 Evaluate side-chains 210 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 2.808 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2243 time to fit residues: 11.1294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 175 optimal weight: 0.4980 chunk 224 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 259 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 186 optimal weight: 0.3980 chunk 141 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26342 Z= 0.165 Angle : 0.553 9.914 35830 Z= 0.272 Chirality : 0.044 0.430 4223 Planarity : 0.004 0.065 4567 Dihedral : 4.141 26.390 3417 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.08 % Allowed : 16.65 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3153 helix: 2.42 (0.20), residues: 666 sheet: 0.13 (0.21), residues: 600 loop : -1.46 (0.13), residues: 1887 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 225 average time/residue: 0.3526 time to fit residues: 132.1284 Evaluate side-chains 206 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 2.810 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2350 time to fit residues: 10.3041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.0670 chunk 194 optimal weight: 0.0000 chunk 208 optimal weight: 0.1980 chunk 151 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 240 optimal weight: 0.0000 overall best weight: 0.1526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 186 ASN B 772 GLN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26342 Z= 0.128 Angle : 0.544 10.329 35830 Z= 0.266 Chirality : 0.044 0.421 4223 Planarity : 0.004 0.064 4567 Dihedral : 4.001 27.291 3417 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.58 % Allowed : 17.26 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3153 helix: 2.78 (0.21), residues: 659 sheet: 0.24 (0.21), residues: 594 loop : -1.35 (0.13), residues: 1900 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 223 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 231 average time/residue: 0.3578 time to fit residues: 136.6811 Evaluate side-chains 199 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 2.743 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2414 time to fit residues: 7.5446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 2.9990 chunk 293 optimal weight: 0.5980 chunk 267 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 171 optimal weight: 0.0970 chunk 124 optimal weight: 10.0000 chunk 224 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 258 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 284 optimal weight: 0.0870 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26342 Z= 0.134 Angle : 0.554 11.007 35830 Z= 0.268 Chirality : 0.044 0.423 4223 Planarity : 0.004 0.065 4567 Dihedral : 3.968 25.755 3417 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.40 % Allowed : 18.23 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3153 helix: 2.86 (0.21), residues: 656 sheet: 0.36 (0.21), residues: 587 loop : -1.35 (0.13), residues: 1910 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 204 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 209 average time/residue: 0.3657 time to fit residues: 128.0053 Evaluate side-chains 196 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 3.200 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2450 time to fit residues: 7.0087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.7980 chunk 302 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 143 optimal weight: 0.0870 chunk 209 optimal weight: 0.6980 chunk 316 optimal weight: 1.9990 chunk 291 optimal weight: 0.0570 chunk 252 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26342 Z= 0.139 Angle : 0.562 11.393 35830 Z= 0.271 Chirality : 0.044 0.422 4223 Planarity : 0.004 0.066 4567 Dihedral : 3.964 30.347 3417 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.22 % Allowed : 18.55 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3153 helix: 2.97 (0.20), residues: 650 sheet: 0.30 (0.21), residues: 609 loop : -1.31 (0.13), residues: 1894 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 206 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 211 average time/residue: 0.3545 time to fit residues: 124.1367 Evaluate side-chains 191 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 188 time to evaluate : 2.918 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2440 time to fit residues: 5.3589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.5980 chunk 268 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 259 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 GLN B 392 ASN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.172984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109056 restraints weight = 41043.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113128 restraints weight = 21842.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115617 restraints weight = 14902.779| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 26342 Z= 0.413 Angle : 0.698 9.854 35830 Z= 0.347 Chirality : 0.048 0.428 4223 Planarity : 0.004 0.064 4567 Dihedral : 4.510 28.610 3417 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.47 % Allowed : 18.88 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3153 helix: 1.95 (0.20), residues: 673 sheet: 0.11 (0.21), residues: 588 loop : -1.55 (0.13), residues: 1892 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4615.94 seconds wall clock time: 85 minutes 48.10 seconds (5148.10 seconds total)