Starting phenix.real_space_refine on Mon Feb 19 06:50:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epp_28532/02_2024/8epp_28532.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epp_28532/02_2024/8epp_28532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epp_28532/02_2024/8epp_28532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epp_28532/02_2024/8epp_28532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epp_28532/02_2024/8epp_28532.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8epp_28532/02_2024/8epp_28532.pdb" } resolution = 3.1 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= 0.002 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 101 5.16 5 C 15231 2.51 5 N 3893 2.21 5 O 4688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 747": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23913 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7926 Classifications: {'peptide': 1009} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 49, 'TRANS': 956} Chain breaks: 9 Chain: "B" Number of atoms: 7648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7648 Classifications: {'peptide': 976} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 926} Chain breaks: 10 Chain: "C" Number of atoms: 7451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7451 Classifications: {'peptide': 954} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 45, 'TRANS': 907} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 12.80, per 1000 atoms: 0.54 Number of scatterers: 23913 At special positions: 0 Unit cell: (148.07, 136.68, 178.89, 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 101 16.00 O 4688 8.00 N 3893 7.00 C 15231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " 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 I 2 " - " BMA I 3 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 616 " " NAG A1204 " - " ASN A 709 " " NAG A1205 " - " ASN A1098 " " NAG A1206 " - " ASN A 165 " " NAG A1207 " - " ASN A 343 " " NAG A1208 " - " ASN A1074 " " NAG B1201 " - " ASN B 234 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 657 " " NAG B1204 " - " ASN B 343 " " NAG B1205 " - " ASN B 709 " " NAG B1206 " - " ASN B 603 " " NAG B1207 " - " ASN B 61 " " NAG C1201 " - " ASN C1074 " " NAG C1202 " - " ASN C1098 " " NAG C1203 " - " ASN C 709 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 343 " " NAG C1207 " - " ASN C 282 " " NAG C1208 " - " ASN C 165 " " NAG C1209 " - " ASN C 234 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 616 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 282 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C 616 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 122 " Time building additional restraints: 11.22 Conformation dependent library (CDL) restraints added in 4.3 seconds 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 49 sheets defined 26.0% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.977A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.705A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.574A pdb=" N GLY A 545 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.615A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 888 removed outlier: 3.902A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 888' Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.581A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.509A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.811A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.534A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.132A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.568A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.520A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.541A pdb=" N VAL B 622 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.611A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.779A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.509A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.119A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.516A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.506A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.027A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.948A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.541A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.645A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.290A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.695A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.551A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.976A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.935A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.850A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.863A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.254A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 325 removed outlier: 4.070A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.153A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.406A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.046A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.514A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.514A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.416A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.941A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.755A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.749A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.545A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 89 through 90 removed outlier: 3.856A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 188 through 190 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.207A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.222A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.548A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.141A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.964A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.426A pdb=" N GLU B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.696A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.763A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.763A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.205A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.618A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.550A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.088A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.971A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 226 through 229 removed outlier: 3.739A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.157A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.609A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.965A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.755A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.755A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.738A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 955 hydrogen bonds defined for protein. 2643 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: 11.47 Time building geometry restraints manager: 11.70 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: 7518 1.34 - 1.46: 4750 1.46 - 1.58: 12033 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 24428 Sorted by residual: bond pdb=" N CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.16e+00 bond pdb=" N ILE A 980 " pdb=" CA ILE A 980 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.49e+00 bond pdb=" N LEU A 984 " pdb=" CA LEU A 984 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.78e+00 bond pdb=" N LYS B 529 " pdb=" CA LYS B 529 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.06e+00 bond pdb=" N LEU A 981 " pdb=" CA LEU A 981 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.28e-02 6.10e+03 5.91e+00 ... (remaining 24423 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.66: 665 106.66 - 113.52: 13638 113.52 - 120.38: 8517 120.38 - 127.24: 10199 127.24 - 134.11: 203 Bond angle restraints: 33222 Sorted by residual: angle pdb=" C HIS C 519 " pdb=" N ALA C 520 " pdb=" CA ALA C 520 " ideal model delta sigma weight residual 121.80 131.42 -9.62 2.44e+00 1.68e-01 1.56e+01 angle pdb=" N GLY C 744 " pdb=" CA GLY C 744 " pdb=" C GLY C 744 " ideal model delta sigma weight residual 111.36 115.40 -4.04 1.17e+00 7.31e-01 1.19e+01 angle pdb=" CA VAL B 524 " pdb=" C VAL B 524 " pdb=" O VAL B 524 " ideal model delta sigma weight residual 121.70 118.09 3.61 1.06e+00 8.90e-01 1.16e+01 angle pdb=" N ARG A 983 " pdb=" CA ARG A 983 " pdb=" C ARG A 983 " ideal model delta sigma weight residual 114.39 109.69 4.70 1.45e+00 4.76e-01 1.05e+01 angle pdb=" CA THR A 912 " pdb=" C THR A 912 " pdb=" O THR A 912 " ideal model delta sigma weight residual 121.87 118.46 3.41 1.10e+00 8.26e-01 9.58e+00 ... (remaining 33217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.95: 14173 21.95 - 43.89: 950 43.89 - 65.84: 188 65.84 - 87.78: 74 87.78 - 109.73: 29 Dihedral angle restraints: 15414 sinusoidal: 6848 harmonic: 8566 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 168.12 -75.12 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 167.80 -74.80 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 161.58 -68.58 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 15411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 3952 0.146 - 0.292: 20 0.292 - 0.437: 6 0.437 - 0.583: 2 0.583 - 0.729: 1 Chirality restraints: 3981 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" C1 NAG A1203 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1203 " pdb=" O5 NAG A1203 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 3978 not shown) Planarity restraints: 4242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.210 9.50e-02 1.11e+02 9.42e-02 5.45e+00 pdb=" NE ARG A 983 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 811 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 812 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 812 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 812 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 64 " 0.012 2.00e-02 2.50e+03 1.16e-02 3.37e+00 pdb=" CG TRP C 64 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP C 64 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 64 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 64 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 64 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 64 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 64 " 0.002 2.00e-02 2.50e+03 ... (remaining 4239 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2564 2.75 - 3.29: 22702 3.29 - 3.83: 38826 3.83 - 4.36: 43460 4.36 - 4.90: 76939 Nonbonded interactions: 184491 Sorted by model distance: nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.217 2.440 nonbonded pdb=" N GLU C 748 " pdb=" OE1 GLU C 748 " model vdw 2.219 2.520 nonbonded pdb=" OE2 GLU A 465 " pdb=" O3 NAG B1201 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR C 761 " pdb=" OE1 GLN C 762 " model vdw 2.233 2.440 nonbonded pdb=" O6 NAG P 1 " pdb=" O5 NAG P 2 " model vdw 2.244 2.440 ... (remaining 184486 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 27 through 69 or resid 78 through 143 or resid 156 through \ 172 or resid 186 through 245 or resid 263 through 438 or resid 508 through 1147 \ or resid 1201 through 1207)) selection = (chain 'B' and (resid 27 through 172 or resid 186 through 438 or resid 508 throu \ gh 1147 or resid 1201 through 1207)) selection = (chain 'C' and (resid 27 through 143 or resid 156 through 1147 or resid 1201 thr \ ough 1207)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'O' } 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: 10.030 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: 29.360 Check model and map are aligned: 0.400 Set scattering table: 0.280 Process input model: 68.200 Find NCS groups from input model: 2.190 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.004 0.052 24428 Z= 0.234 Angle : 0.586 9.624 33222 Z= 0.292 Chirality : 0.050 0.729 3981 Planarity : 0.004 0.094 4203 Dihedral : 16.166 109.727 9778 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.65 % Favored : 96.21 % Rotamer: Outliers : 0.35 % Allowed : 13.13 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2879 helix: 2.69 (0.21), residues: 663 sheet: -0.10 (0.22), residues: 554 loop : -1.01 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 64 HIS 0.003 0.000 HIS B 207 PHE 0.010 0.001 PHE C 140 TYR 0.013 0.001 TYR A 695 ARG 0.002 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 71 average time/residue: 0.3280 time to fit residues: 41.7121 Evaluate side-chains 66 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 1121 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 6.9990 chunk 221 optimal weight: 0.0030 chunk 122 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 228 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 30.0000 chunk 170 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 115 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 314 GLN A 613 GLN A 641 ASN A 895 GLN B 66 HIS B 125 ASN B 207 HIS B 245 HIS B 564 GLN B 920 GLN B1011 GLN B1048 HIS B1083 HIS C 134 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 437 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1084 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24428 Z= 0.331 Angle : 0.617 10.060 33222 Z= 0.317 Chirality : 0.049 0.504 3981 Planarity : 0.004 0.041 4203 Dihedral : 10.439 78.900 4514 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.62 % Rotamer: Outliers : 2.81 % Allowed : 12.94 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: -0.01 (0.16), residues: 2879 helix: 2.42 (0.21), residues: 679 sheet: -0.02 (0.21), residues: 625 loop : -1.14 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.005 0.001 HIS C1058 PHE 0.017 0.002 PHE C1089 TYR 0.030 0.002 TYR B 674 ARG 0.003 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 63 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7634 (mp) REVERT: A 429 PHE cc_start: 0.3995 (t80) cc_final: 0.3779 (t80) REVERT: A 1115 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7890 (mm) REVERT: B 65 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7251 (t80) REVERT: B 131 CYS cc_start: 0.4505 (OUTLIER) cc_final: 0.4187 (m) REVERT: B 853 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: C 96 GLU cc_start: 0.4799 (OUTLIER) cc_final: 0.4562 (pt0) REVERT: C 134 GLN cc_start: 0.4661 (tp40) cc_final: 0.4339 (tp-100) REVERT: C 244 LEU cc_start: 0.7041 (tp) cc_final: 0.6647 (pt) outliers start: 72 outliers final: 38 residues processed: 130 average time/residue: 0.2890 time to fit residues: 66.6783 Evaluate side-chains 101 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 57 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1121 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 286 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 121 ASN B1083 HIS C 239 GLN C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24428 Z= 0.244 Angle : 0.570 9.958 33222 Z= 0.292 Chirality : 0.048 0.480 3981 Planarity : 0.004 0.041 4203 Dihedral : 9.317 74.750 4505 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 2.88 % Allowed : 13.91 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 0.01 (0.16), residues: 2879 helix: 2.48 (0.21), residues: 679 sheet: -0.03 (0.20), residues: 626 loop : -1.14 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 104 HIS 0.004 0.001 HIS C1083 PHE 0.018 0.001 PHE C 392 TYR 0.022 0.001 TYR B 170 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 59 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7946 (mm) REVERT: B 65 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7338 (t80) REVERT: B 287 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: B 938 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8888 (tt) REVERT: C 96 GLU cc_start: 0.4815 (OUTLIER) cc_final: 0.4597 (pt0) REVERT: C 134 GLN cc_start: 0.4795 (tp40) cc_final: 0.4496 (tp-100) REVERT: C 141 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5747 (pt) REVERT: C 244 LEU cc_start: 0.7142 (tp) cc_final: 0.6629 (pt) outliers start: 74 outliers final: 45 residues processed: 128 average time/residue: 0.2895 time to fit residues: 66.4160 Evaluate side-chains 107 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 56 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 266 optimal weight: 0.4980 chunk 282 optimal weight: 4.9990 chunk 139 optimal weight: 30.0000 chunk 252 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24428 Z= 0.212 Angle : 0.548 9.882 33222 Z= 0.280 Chirality : 0.047 0.479 3981 Planarity : 0.004 0.042 4203 Dihedral : 8.534 70.272 4503 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 3.23 % Allowed : 14.30 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2879 helix: 2.55 (0.21), residues: 679 sheet: -0.00 (0.20), residues: 628 loop : -1.13 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS C1083 PHE 0.014 0.001 PHE C1121 TYR 0.015 0.001 TYR B 170 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 57 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7613 (tp) REVERT: A 191 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: A 1115 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7951 (mm) REVERT: B 65 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7373 (t80) REVERT: B 287 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: B 938 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8879 (tt) REVERT: C 96 GLU cc_start: 0.4865 (OUTLIER) cc_final: 0.4659 (pt0) REVERT: C 134 GLN cc_start: 0.4792 (tp40) cc_final: 0.4424 (tp-100) REVERT: C 141 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5758 (pt) REVERT: C 244 LEU cc_start: 0.7003 (tp) cc_final: 0.6500 (pt) outliers start: 83 outliers final: 58 residues processed: 136 average time/residue: 0.3090 time to fit residues: 74.1468 Evaluate side-chains 120 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 54 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS C 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24428 Z= 0.157 Angle : 0.522 10.189 33222 Z= 0.265 Chirality : 0.047 0.470 3981 Planarity : 0.003 0.042 4203 Dihedral : 7.747 65.416 4501 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 3.08 % Allowed : 14.65 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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 (0.16), residues: 2879 helix: 2.68 (0.21), residues: 680 sheet: 0.01 (0.20), residues: 620 loop : -1.09 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.004 0.001 HIS A 207 PHE 0.013 0.001 PHE C 135 TYR 0.014 0.001 TYR B 170 ARG 0.002 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 58 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 LEU cc_start: 0.8353 (pp) cc_final: 0.7923 (tp) REVERT: A 1115 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7979 (mm) REVERT: B 65 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7455 (t80) REVERT: B 287 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: B 938 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8841 (tt) REVERT: C 96 GLU cc_start: 0.4910 (OUTLIER) cc_final: 0.4692 (pt0) REVERT: C 134 GLN cc_start: 0.4886 (tp40) cc_final: 0.4608 (tp-100) REVERT: C 141 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5679 (mm) REVERT: C 244 LEU cc_start: 0.7061 (tp) cc_final: 0.6773 (pt) REVERT: C 612 TYR cc_start: 0.6323 (OUTLIER) cc_final: 0.6020 (p90) outliers start: 79 outliers final: 52 residues processed: 131 average time/residue: 0.3107 time to fit residues: 73.0017 Evaluate side-chains 115 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 56 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 282 optimal weight: 0.6980 chunk 234 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 148 optimal weight: 0.3980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24428 Z= 0.203 Angle : 0.530 9.946 33222 Z= 0.270 Chirality : 0.046 0.474 3981 Planarity : 0.004 0.042 4203 Dihedral : 7.401 62.175 4501 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 3.27 % Allowed : 14.58 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 0.15 (0.16), residues: 2879 helix: 2.72 (0.21), residues: 674 sheet: 0.05 (0.20), residues: 622 loop : -1.10 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.009 0.001 HIS A 207 PHE 0.013 0.001 PHE B 541 TYR 0.014 0.001 TYR C1067 ARG 0.004 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 55 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 LEU cc_start: 0.8384 (pp) cc_final: 0.7986 (tp) REVERT: A 1115 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7937 (mm) REVERT: B 65 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7487 (t80) REVERT: B 287 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: B 938 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8858 (tt) REVERT: C 96 GLU cc_start: 0.4976 (OUTLIER) cc_final: 0.4733 (pt0) REVERT: C 134 GLN cc_start: 0.4876 (tp40) cc_final: 0.4582 (tp40) REVERT: C 135 PHE cc_start: 0.5233 (m-80) cc_final: 0.4804 (m-80) outliers start: 84 outliers final: 72 residues processed: 135 average time/residue: 0.2715 time to fit residues: 65.6638 Evaluate side-chains 132 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 55 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 237 optimal weight: 0.0370 chunk 157 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 171 optimal weight: 0.0570 chunk 129 optimal weight: 20.0000 overall best weight: 2.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24428 Z= 0.261 Angle : 0.561 10.016 33222 Z= 0.285 Chirality : 0.047 0.476 3981 Planarity : 0.004 0.042 4203 Dihedral : 7.218 58.997 4501 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.00 % Rotamer: Outliers : 3.55 % Allowed : 14.61 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 0.06 (0.16), residues: 2879 helix: 2.65 (0.21), residues: 673 sheet: -0.02 (0.20), residues: 617 loop : -1.14 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.014 0.001 HIS A 207 PHE 0.014 0.001 PHE B 541 TYR 0.015 0.001 TYR C1067 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 60 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 LEU cc_start: 0.8429 (pp) cc_final: 0.8039 (tp) REVERT: A 983 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7557 (ttp-170) REVERT: A 1115 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.7909 (mm) REVERT: B 65 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7438 (t80) REVERT: B 287 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7784 (m-30) REVERT: C 96 GLU cc_start: 0.4994 (OUTLIER) cc_final: 0.4698 (pt0) REVERT: C 134 GLN cc_start: 0.4874 (tp40) cc_final: 0.4589 (tp40) REVERT: C 135 PHE cc_start: 0.5176 (m-80) cc_final: 0.4756 (m-80) outliers start: 91 outliers final: 78 residues processed: 147 average time/residue: 0.2969 time to fit residues: 75.7748 Evaluate side-chains 141 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 58 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 0.0670 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 139 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 221 optimal weight: 0.0170 overall best weight: 1.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24428 Z= 0.160 Angle : 0.527 9.930 33222 Z= 0.267 Chirality : 0.047 0.554 3981 Planarity : 0.003 0.042 4203 Dihedral : 6.838 58.274 4501 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 3.23 % Allowed : 14.96 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.15 (0.16), residues: 2879 helix: 2.72 (0.21), residues: 675 sheet: 0.04 (0.20), residues: 629 loop : -1.10 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.016 0.001 HIS A 207 PHE 0.011 0.001 PHE B 541 TYR 0.021 0.001 TYR B 170 ARG 0.002 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 65 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 LEU cc_start: 0.8451 (pp) cc_final: 0.8074 (tp) REVERT: A 1115 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7963 (mm) REVERT: B 65 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7463 (t80) REVERT: B 287 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: B 938 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8843 (tt) REVERT: C 96 GLU cc_start: 0.4978 (OUTLIER) cc_final: 0.4720 (pt0) REVERT: C 134 GLN cc_start: 0.4923 (tp40) cc_final: 0.4655 (tp40) REVERT: C 135 PHE cc_start: 0.5244 (m-80) cc_final: 0.4851 (m-80) REVERT: C 244 LEU cc_start: 0.6822 (tp) cc_final: 0.6417 (mp) REVERT: C 612 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.5955 (p90) REVERT: C 657 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7431 (p0) REVERT: C 748 GLU cc_start: 0.8579 (pm20) cc_final: 0.8354 (pm20) outliers start: 83 outliers final: 71 residues processed: 144 average time/residue: 0.2958 time to fit residues: 75.6359 Evaluate side-chains 139 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 61 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 245 optimal weight: 0.0870 chunk 262 optimal weight: 0.0010 chunk 157 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 overall best weight: 1.7968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24428 Z= 0.187 Angle : 0.531 9.969 33222 Z= 0.269 Chirality : 0.046 0.462 3981 Planarity : 0.003 0.042 4203 Dihedral : 6.588 58.859 4501 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 3.27 % Allowed : 15.00 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 0.13 (0.16), residues: 2879 helix: 2.70 (0.21), residues: 679 sheet: 0.01 (0.20), residues: 632 loop : -1.12 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.006 0.001 HIS A 207 PHE 0.012 0.001 PHE B 541 TYR 0.019 0.001 TYR B 170 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 60 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 LEU cc_start: 0.8448 (pp) cc_final: 0.8073 (tp) REVERT: A 1115 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7927 (mm) REVERT: B 65 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7485 (t80) REVERT: B 287 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: B 938 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8837 (tt) REVERT: C 96 GLU cc_start: 0.4996 (OUTLIER) cc_final: 0.4708 (pt0) REVERT: C 134 GLN cc_start: 0.4852 (tp40) cc_final: 0.4594 (tp40) REVERT: C 135 PHE cc_start: 0.4977 (m-80) cc_final: 0.4540 (m-80) REVERT: C 612 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.5920 (p90) REVERT: C 657 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7430 (p0) outliers start: 84 outliers final: 74 residues processed: 140 average time/residue: 0.2855 time to fit residues: 70.8187 Evaluate side-chains 139 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 58 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 0.8980 chunk 277 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 131 optimal weight: 0.0770 chunk 192 optimal weight: 0.9990 chunk 290 optimal weight: 0.0770 chunk 267 optimal weight: 3.9990 chunk 231 optimal weight: 40.0000 chunk 24 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24428 Z= 0.138 Angle : 0.510 9.918 33222 Z= 0.258 Chirality : 0.046 0.447 3981 Planarity : 0.003 0.042 4203 Dihedral : 6.247 58.086 4501 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 2.96 % Allowed : 15.28 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 0.20 (0.16), residues: 2879 helix: 2.82 (0.21), residues: 675 sheet: 0.05 (0.21), residues: 626 loop : -1.08 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.017 0.001 HIS A 207 PHE 0.013 0.001 PHE A 429 TYR 0.020 0.001 TYR B 170 ARG 0.002 0.000 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 63 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 LEU cc_start: 0.8465 (pp) cc_final: 0.8099 (tp) REVERT: B 65 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7529 (t80) REVERT: B 287 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: B 938 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8906 (tt) REVERT: C 96 GLU cc_start: 0.5071 (OUTLIER) cc_final: 0.4765 (pt0) REVERT: C 134 GLN cc_start: 0.4900 (tp40) cc_final: 0.4666 (tp40) REVERT: C 135 PHE cc_start: 0.4922 (m-80) cc_final: 0.4498 (m-80) REVERT: C 612 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.5871 (p90) REVERT: C 657 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7409 (p0) REVERT: C 748 GLU cc_start: 0.8585 (pm20) cc_final: 0.8367 (pm20) outliers start: 76 outliers final: 67 residues processed: 135 average time/residue: 0.2966 time to fit residues: 70.4133 Evaluate side-chains 135 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 62 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 34 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 232 optimal weight: 30.0000 chunk 97 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 29 optimal weight: 0.0010 chunk 42 optimal weight: 20.0000 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.099387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.065757 restraints weight = 99521.690| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 5.79 r_work: 0.3202 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24428 Z= 0.183 Angle : 0.521 9.976 33222 Z= 0.264 Chirality : 0.046 0.445 3981 Planarity : 0.003 0.042 4203 Dihedral : 6.149 58.570 4501 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.48 % Favored : 95.45 % Rotamer: Outliers : 3.08 % Allowed : 15.35 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 0.17 (0.16), residues: 2879 helix: 2.73 (0.21), residues: 680 sheet: 0.03 (0.21), residues: 626 loop : -1.08 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 104 HIS 0.007 0.001 HIS A 207 PHE 0.011 0.001 PHE B 541 TYR 0.019 0.001 TYR B 170 ARG 0.002 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5293.55 seconds wall clock time: 98 minutes 3.44 seconds (5883.44 seconds total)